7A20

Azobenzene-Based Inhibitors for Tryptophan Synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.190 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Towards Photochromic Azobenzene-Based Inhibitors for Tryptophan Synthase.

Simeth, N.A.Kinateder, T.Rajendran, C.Nazet, J.Merkl, R.Sterner, R.Konig, B.Kneuttinger, A.C.

(2021) Chemistry 27: 2439-2451

  • DOI: https://doi.org/10.1002/chem.202004061
  • Primary Citation of Related Structures:  
    7A20

  • PubMed Abstract: 

    Light regulation of drug molecules has gained growing interest in biochemical and pharmacological research in recent years. In addition, a serious need for novel molecular targets of antibiotics has emerged presently. Herein, the development of a photocontrollable, azobenzene-based antibiotic precursor towards tryptophan synthase (TS), an essential metabolic multienzyme complex in bacteria, is presented. The compound exhibited moderately strong inhibition of TS in its E configuration and five times lower inhibition strength in its Z configuration. A combination of biochemical, crystallographic, and computational analyses was used to characterize the inhibition mode of this compound. Remarkably, binding of the inhibitor to a hitherto-unconsidered cavity results in an unproductive conformation of TS leading to noncompetitive inhibition of tryptophan production. In conclusion, we created a promising lead compound for combatting bacterial diseases, which targets an essential metabolic enzyme, and whose inhibition strength can be controlled with light.


  • Organizational Affiliation

    Institute for Organic Chemistry, Department of Chemistry and Pharmacy, University of Regensburg, Universitätsstrasse 31, 93040, Regensburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tryptophan synthase alpha chain,Tryptophan synthase beta chain
A, B, C, D
709Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: 
trpAA2O69_02705A3104_03440A3111_06745A3122_00255A3146_03380A3R41_00165A3S30_00165A3T21_03455A3T81_00165A3U32_00150A3V03_00165A3V89_11045A3W57_00165A3W75_00165A3W86_01965A3X15_04675A3X55_12365A3Y76_02020A3Z96_03140A4J27_03515A4N07_00165A4O05_04690A4O41_00150A4R48_02635A6D61_00170A9C21_03190A9T39_18105A9U46_07410A9U64_18365AAA76_00150AAB27_09270AAB39_14810AAB79_17605AAC08_07455AAC35_00165AAC42_18410AAC44_05105AAC95_06065AAC98_13025AAP89_02040AAQ24_17995AB424_02950ABO94_19165ABP11_12170ABP54_18790ABP87_03850ABQ69_14875ADQ28_02555ADQ45_00240AE787_02705AF480_03970AF488_06010AF489_02665AF497_08115AGC55_13730AGM99_16795AGQ32_20570AH984_18390AHN93_02390AIC76_02220AKH62_04250AKH68_02485AKI16_02905AL144_16655AL151_17295AL154_21000AL166_18245AL168_15620AL170_16745AL174_09875AL184_20195APP08_15525APY91_03770AQ530_01185AS118_02485AT354_12420AU613_22480AU805_00165AU830_08695AU839_18250AU951_15150AU965_03075AVA38_22265AVB77_10095AVB94_04695AVC05_15210AVC09_12505AVD08_21490AVD75_00165AVD94_08010AVG17_00165AVL02_12425AVL16_02485AVM19_00175AWT30_03275AXM10_01875AXM23_01440AXR84_21845AXU58_18715AXX99_00240B1265_17725B1398_17375B1642_03095B1B86_18920B1B89_03520B1I91_02735B1P38_14645B1Q82_16840B2E31_01135B4V59_01135B4W90_02485B5A40_16835B6362_18045B6G98_13730B6M25_03795B6M43_05330B7071_04190B7890_00175B7J30_16895B7Q27_19120B8Y16_01435B8Y36_00155B8Z46_02485B9653_00865B9C61_00150B9C71_05000B9C90_02620B9C91_02590B9C96_00165B9M14_03095B9O84_04985B9U29_02985BBQ66_00240BEL47_09235BFE55_13565BFE61_16675BGP52_00165BIC00_16195BIC01_10580BIC03_16625BIC13_14195BJP89_17195BK110_16900BKM50_00475BLB03_15980BMG85_08675BMS46_07365BMU56_00240BSC80_03845BSD55_03840BZ203_00605BZ210_00240BZG47_02665BZN20_03405BZZ88_16725C4E88_03760C5U54_03945C5W43_02665CA117_01345CB102_03620CB119_10845CB161_01680CB198_15690CB380_00165CB383_15120CB416_01750CB530_00165CB535_01775CB570_06130CB646_05190CB657_17400CBH20_00175CBM40_00165CBM67_00165CBM76_00165CBN77_01660CBO42_03385CBR08_18060CBU32_02805CBZ90_16170CC339_09500CC403_14740CC453_16025CC594_08910CC652_03220CC725_00150CC886_03025CC918_08535CC944_16230CC971_02325CCF93_01195CCP17_15500CCW27_18535CD48_01250CD977_00550CDJ75_00180CDT37_16830CDZ72_11625CE355_01005CE615_00485CE70_00970CE806_19050CE87_00485CE896_13660CEC46_02430CEC56_00175CED07_00240CEQ70_19135CER60_14705CER78_02655CET98_00485CEY64_04075CFB16_19755CFB28_02665CFE76_03605CFE79_19510CFF58_02665CFF59_02525CFJ48_19420CGG73_00630CHN22_02485CI444_00485CIX60_05920CJC42_00250CPR79_00165CPS79_00170CPX68_00150CQE35_02200CQG18_02720CQO33_05130CR370_00805CRB02_00250CSG22_09805CTJ81_13370CVR97_02980D3147_03405D3174_02065D3F31_17940D3T68_17465D3Y48_10480D4361_01915D4369_03490D4380_02475D4387_05635D4422_03585D4E62_00150D4E68_07205D4E74_05085D4X64_05240D4X79_00155D4Y62_02075D5823_04015D5949_01700D5B48_00165D5C67_05335D5C71_03580D5N86_03365D5N95_03775D5O82_00165D5P17_00170D5X47_00150D5Y28_01995D6360_05130D6367_06235D6371_00165D6373_01595D6395_18515D6421_01595D6422_13005D6J79_06095D6K10_14630D6P67_05625D6Q64_00165D6S43_00165D6T00_04260D6T40_02400D7F20_01775D7H43_22435D7N92_00165D7O44_03135D8Q90_00150D8S24_03725D9O84_00165DD95_04145DJ388_09095DJ702_07165DK061_00165DK631_13465DK641_13520DK642_09860DK689_04165DK696_00150DK698_07510DKJ10_06065DKR95_00175DKS55_13070DKU45_00165DKU57_01735DKU80_09485DLB14_00165DLB57_04215DLB93_03780DLR28_07050DM322_07700DMI89_03520DMO92_04580DMV40_19515DMZ93_09320DN165_02740DN204_04800DN359_09810DN904_05240DNB97_02890DNL62_13145DNM27_00165DNM63_00165DNU59_01730DNV08_02460DNV12_06765DNV30_02645DNY92_05155DNZ37_13565DO350_14190DO533_00150DO585_06990DO640_03040DO698_02860DO766_01990DO828_00165DO960_02185DOC60_08275DOH72_01750DOI32_03375DOI53_01965DOI92_02215DOJ39_00165DOJ91_00995DOQ54_00160DOQ88_05390DOR12_01815DOV43_07015DOW25_01945DP680_05135DPB42_18060DPB45_01835DPB48_03655DPB57_00470DPD91_03680DPD95_01730DPD99_16165DPF41_04660DPF68_00165DPK32_00170DPK79_00165DPL02_00245DPP94_16890DPP97_00165DPS76_03535DPT18_00165DPU20_00150DPY58_03125DQ848_22180DQ947_07370DQ951_00165DQC39_04655DQC52_04020DQD03_00165DQD22_02710DQE64_05325DQE65_07775DQK42_00165DQQ98_01485DQR10_06595DQR44_00155DQR61_14685DQS14_15275DQY10_00175DQZ46_17880DQZ56_00165DR982_04290DRL45_00165DRM14_00165DRM16_05695DRR75_10995DRT38_04265DRT61_09470DRT65_11175DRV05_00150DRW84_00160DRX66_18265DS270_00160DS296_18550DS451_00160DS453_03510DS521_00165DS619_01750DSF69_00165DSF94_07465DSG41_00165DSM38_03595DSN15_07075DSR36_00150DTE73_04565DTF68_04450DTG22_18830DTG27_10390DTW13_02010DTW14_04720DTW26_04250DU071_15075DU223_01835DU657_05890DU821_03570DU879_04025DU924_01705DUQ28_05205DUQ56_02015DUQ92_13425DUR36_02790DUV75_02775DUW10_00165DUW48_00165DVF14_00165DVF88_01725DVG01_03395DVZ53_00975DWU22_05275DY580_18355DYM27_15965DYS82_04400DZG11_04030E0584_04235E0595_03330E0935_04470E0989_02695E0M34_03825E0U75_00170E0V94_01720E1A11_00170E1A20_21775E5196_00315E6W45_19445EBB93_00165EBC01_00250EBD14_01910EBD99_05485EBK21_00170EBL31_00490EBO41_01945EBP31_03915EC404_00170EC52_01135ECA50_02905ECC89_03730ED424_01895ED467_02970EDL18_05825EEK73_02635EEQ30_08390EER35_12060EGL32_03685EGN81_18585EGU67_04970EGU98_07510EHB09_01395EHB24_02710EHB55_00165EHC98_05580EIE48_00170EIW53_01740EJI18_00155EJO08_03325EJO98_00565EKA25_00510EL822_00175ELO47_03140ELR28_01915ELS01_00155EM832_04940EM840_00165EMN66_03650EMY79_01615EO190_03990EP115_03025EP446_10220EPB30_00170EPH81_02040EQG93_01815EQG94_00165ERM04_00170EU306_00165EU349_00155EU873_02915EUB95_14525EUQ56_04025EUQ65_02365EUQ74_06790EUS13_04110EVY71_00180EW905_13420EWB18_18055EWE52_00155EWJ47_00250EWZ09_03885EXA47_00250EXB31_22555EXB41_01725EYA29_11485EYJ91_04470F0D96_02435F2O93_00605F2P00_03530F3Q46_10710F3Q58_08080F3Q59_08000F3Q88_02705F3Q97_02930F3R12_00170F3R61_03870F3R63_00160F7773_04550F9G02_00150F9O44_16545FE758_04145FEM52_02630FGZ46_01675FJM64_00165FL833_00150FQC24_03100FQD13_06725GCH31_00150GCQ81_00165GEZ01_04015GW08_03170JO10_00485KP44_16040LZ63_02665NG02_04170NG06_16725NG18_14005NU83_02665QA89_14460QB40_00165QD15_05220R035_09170RJ78_16495SAMEA4398682_02246SE14_01811Y934_00970YG50_13190YR17_00165Z700_00165ZB89_05450ZC54_00165ZT09_07605ZT28_00160ZT74_16545ZT89_11220ZU86_12130ZU92_17275ZV06_15530ZV17_18190ZV33_00160ZV34_00165ZV38_00165ZV58_05875ZV70_10430ZV76_15960ZV78_00160ZV90_13180ZW74_18835ZX03_08395ZY23_01875ZY27_00165ZY40_08865ZY51_17020ZZ18_11975ZZ43_16745ZZ77_00150ZZ79_17010trpBA2O69_02700A3104_03435A3111_06740A3122_00260A3146_03375A3R41_00170A3S30_00170A3T21_03460A3T81_00170A3U32_00155A3V03_00170A3V89_11050A3W57_00170A3W86_01970A3X15_04680A3X55_12370A3Y76_02015A3Z96_03135A4J27_03520A4N07_00170A4O05_04695A4O41_00155A4R48_02630A6D61_00175A9C21_03185A9T39_18110A9U46_07415A9U64_18370AAA76_00155AAB27_09275AAB39_14815AAB79_17610AAC08_07460AAC35_00170AAC42_18415AAC44_05110AAC95_06070AAC98_13030AAP89_02045AAQ24_18000AB424_02945ABO94_19170ABP11_12175ABP54_18795ABP87_03855ABQ69_14880ADQ28_02550ADQ45_00245AE787_02700AF480_03975AF488_06015AF489_02660AF497_08120AGC55_13735AGM99_16800AGQ32_20575AH984_18395AHN93_02395AIC76_02215AKH62_04245AKH68_02480AKI16_02910AL144_16660AL151_17300AL166_18250AL168_15625AL170_16750AL174_09880AL184_20200APP08_15530APY91_03765AQ530_01180AS118_02480AT354_12415AU613_22485AU805_00170AU830_08700AU839_18255AU951_15155AU965_03080AVA38_22260AVB77_10100AVB94_04700AVC05_15215AVD75_00170AVD94_08015AVG17_00170AVL02_12430AVL16_02480AVM19_00180AWT30_03270AXM10_01880AXM23_01435AXR84_21850AXU58_18720AXX99_00245B1265_17730B1398_17380B1642_03090B1B86_18925B1B89_03525B1I91_02730B1P38_14650B1Q82_16845B2E31_01130B4V59_01130B4W90_02480B5A40_16840B6362_18050B6G98_13735B6M25_03790B6M43_05335B7071_04185B7890_00180B7J30_16900B7Q27_19125B8Y16_01430B8Y36_00160B8Z46_02480B9653_00860B9C61_00155B9C71_05005B9C90_02615B9C91_02585B9C96_00170B9M14_03090B9O84_04980B9U29_02980BBQ66_00245BEL47_09240BFE55_13570BFE61_16680BGP52_00170BIC00_16200BIC01_10585BIC03_16630BIC13_14200BJP89_17200BK110_16905BKM50_00480BLB03_15985BMG85_08680BMS46_07360BMU56_00245BSC80_03850BSD55_03835BZ203_00610BZ210_00245BZG47_02660BZN20_03410BZZ88_16730C4E88_03765C5W43_02660CA117_01340CB102_03625CB119_10850CB161_01685CB198_15695CB380_00170CB383_15125CB416_01745CB530_00170CB535_01780CB570_06135CB646_05195CB657_17405CBH20_00180CBM40_00170CBM67_00170CBM76_00170CBN77_01665CBO42_03390CBR08_18065CBU32_02810CBZ90_16175CC339_09505CC403_14745CC453_16030CC594_08915CC652_03225CC725_00155CC886_03030CC918_08540CC944_16235CC971_02330CCF93_01200CCP17_15505CCW27_18540CD48_01255CD977_00555CDJ75_00185CDT37_16835CDZ72_11630CE355_01000CE615_00490CE70_00965CE806_19055CE87_00490CE896_13665CEC46_02425CEC56_00180CED07_00245CEQ70_19140CER60_14710CER78_02650CET98_00490CEY64_04070CFB16_19760CFB28_02660CFE76_03600CFE79_19515CFF58_02660CFF59_02520CFJ48_19425CGG73_00635CHN22_02480CI444_00490CIX60_05915CJC42_00255CPR79_00170CPS79_00175CPX68_00155CQE35_02195CQG18_02715CQO33_05135CR370_00800CR439_06560CRB02_00255CSG22_09800CTJ81_13375CVR97_02985D3147_03410D3174_02070D3F31_17945D3T68_17470D3Y48_10485D4361_01920D4369_03495D4380_02480D4387_05640D4422_03590D4E62_00155D4E68_07210D4E74_05090D4X64_05245D4X79_00160D4Y62_02080D5823_04020D5949_01705D5B48_00170D5C67_05340D5C71_03585D5N86_03370D5N95_03780D5O82_00170D5P17_00175D5X47_00155D5Y28_02000D6360_05135D6367_06240D6371_00170D6373_01600D6395_18520D6421_01600D6422_13010D6J79_06100D6K10_14635D6P67_05630D6Q64_00170D6S43_00170D6T00_04265D6T40_02405D7F20_01770D7H43_22440D7N92_00170D7O44_03140D8Q90_00155D8S24_03730D9O84_00170DD95_04150DJ388_09100DJ702_07170DK061_00170DK631_13470DK641_13525DK642_09865DK689_04170DK696_00155DK698_07515DKJ10_06070DKR95_00180DKS55_13075DKU45_00170DKU57_01740DKU80_09490DLB14_00170DLB57_04220DLB93_03785DLR28_07055DM322_07705DMO92_04585DMV40_19520DMZ93_09325DN165_02735DN204_04805DN359_09815DN904_05235DNB97_02885DNL62_13150DNM27_00170DNM63_00170DNU59_01735DNV08_02465DNV12_06770DNV30_02640DNY92_05160DNZ37_13570DO350_14195DO533_00155DO585_06995DO640_03045DO698_02865DO766_01995DO828_00170DO960_02190DOC60_08280DOH72_01755DOI32_03380DOI53_01970DOI92_02220DOJ39_00170DOJ91_01000DOQ54_00165DOQ88_05395DOR12_01820DOV43_07020DOW25_01950DP680_05140DPB42_18065DPB45_01840DPB48_03660DPB57_00475DPD91_03685DPD95_01735DPD99_16170DPF41_04665DPF68_00170DPK32_00175DPK79_00170DPL02_00250DPP94_16895DPP97_00170DPS76_03540DPT18_00170DPU20_00155DPY58_03130DQ848_22185DQ947_07375DQ951_00170DQC39_04660DQC52_04025DQD03_00170DQD22_02705DQE64_05330DQE65_07780DQK42_00170DQQ98_01490DQR10_06600DQR44_00160DQR61_14690DQS14_15280DQY10_00180DQZ46_17885DQZ56_00170DR982_04285DRL45_00170DRM14_00170DRM16_05700DRR75_11000DRT38_04270DRT61_09475DRT65_11180DRV05_00155DRW84_00165DRX66_18270DS270_00165DS296_18555DS451_00165DS453_03515DS521_00170DS619_01755DSF69_00170DSF94_07470DSG41_00170DSM38_03600DSN15_07080DSR36_00155DTE73_04570DTF68_04455DTG22_18835DTG27_10395DTW13_02015DTW14_04725DTW26_04255DU071_15080DU223_01840DU657_05885DU821_03575DU879_04030DU924_01710DUQ28_05210DUQ56_02020DUQ92_13430DUR36_02795DUV75_02780DUW10_00170DUW48_00170DVF14_00170DVG01_03400DVZ53_00970DWU22_05270DY580_18360DYM27_15970DYS82_04405DZG11_04025E0595_03335E0935_04475E0989_02690E0M34_03830E0U75_00175E0V94_01725E1A11_00175E1A20_21780E5196_00320E6W45_19450EBB93_00170EBC01_00255EBD14_01915EBD99_05490EBK21_00175EBL31_00495EBO41_01950EBP31_03920EC404_00175EC52_01130ECA50_02910ECC89_03735ED424_01900ED467_02975EDL18_05830EEK73_02630EEQ30_08395EER35_12065EGL32_03690EGN81_18590EGU67_04975EGU98_07515EHB09_01390EHB24_02705EHB55_00170EHC98_05585EIE48_00175EIW53_01745EJI18_00160EJO08_03330EJO98_00570EKA25_00505EL822_00180ELO47_03135ELR28_01920ELS01_00160EM832_04945EM840_00170EMN66_03645EMY79_01620EO190_03995EP115_03030EP446_10225EPB30_00175EPH81_02045EQG93_01820EQG94_00170ERM04_00175EU306_00170EU349_00160EU873_02910EUB95_14530EUQ56_04030EUQ65_02370EUQ74_06795EUS13_04115EVY71_00185EW905_13425EWB18_18060EWE52_00160EWJ47_00255EWZ09_03890EXA47_00255EXB41_01730EYA29_11490EYJ91_04475F0D96_02430F2O93_00610F2P00_03525F3Q46_10715F3Q58_08085F3Q59_08005F3Q88_02710F3Q97_02935F3R12_00175F3R61_03875F3R63_00165F7773_04555F9G02_00155F9O44_16550FE758_04150FEM52_02625FGZ46_01680FJM64_00170FL833_00155FQC24_03095FQD13_06720FQX78_06105GCH31_00155GCQ81_00170GCZ80_03085GEZ01_04020GW08_03175JO10_00490KP44_16045LZ63_02660NG02_04175NG06_16730NG18_14010NU83_02660QA89_14465QB40_00170QD15_05225R035_09175RJ78_16500SAMEA4398682_02247SE14_01810Y934_00965YG50_13195YR17_00170YT65_03520Z700_00170ZB89_05455ZC54_00170ZT09_07610ZT28_00165ZT74_16550ZT89_11225ZU86_12135ZU92_17280ZV06_15535ZV17_18195ZV33_00165ZV34_00170ZV38_00170ZV58_05880ZV70_10435ZV76_15965ZV78_00165ZV90_13185ZW74_18840ZX03_08400ZY23_01880ZY27_00170ZY40_08870ZY51_17025ZZ18_11980ZZ43_16750ZZ77_00155ZZ79_17015

EC: 4.2.1.20
UniProt
Find proteins for P0A2K1 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P0A2K1 
Go to UniProtKB:  P0A2K1
Find proteins for P00929 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P00929 
Go to UniProtKB:  P00929
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0A2K1P00929
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.368α = 90
b = 95.968β = 90
c = 184.719γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySTE 891/12-1

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2021-03-03
    Changes: Database references
  • Version 1.2: 2021-08-04
    Changes: Derived calculations
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references