2CJF | pdb_00002cjf

TYPE II DEHYDROQUINASE INHIBITOR COMPLEX

PDB DOI: https://doi.org/10.2210/pdb2CJF/pdb

Classification: LYASE
Organism(s): Streptomyces coelicolor
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2006-03-31 Released: 2007-04-10
Deposition Author(s): Payne, R.J., Riboldi-Tunnicliffe, A., Abell, A.D., Lapthorn, A.J., Abell, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.334 (Depositor), 0.301 (DCC)
R-Value Work:
0.274 (Depositor), 0.298 (DCC)
R-Value Observed:
0.277 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Design, synthesis, and structural studies on potent biaryl inhibitors of type II dehydroquinases.

Payne, R.J., Riboldi-Tunnicliffe, A., Kerbarh, O., Abell, A.D., Lapthorn, A.J., Abell, C.

(2007) ChemMedChem 2: 1010-1013

PubMed: 17487901 Search on PubMed
DOI: https://doi.org/10.1002/cmdc.200700062
Primary Citation Related Structures:
2CJF

Organizational Affiliation

Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK.

Macromolecule Content

Total Structure Weight: 206.68 kDa
Atom Count: 15,510
Modeled Residue Count: 1,788
Deposited Residue Count: 1,884
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-DEHYDROQUINATE DEHYDRATASE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	157	Streptomyces coelicolor	Mutation(s): 0 EC: 4.2.1.10
UniProt
Find proteins for P15474 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore P15474 Go to UniProtKB: P15474
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15474
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RP4 Query on RP4 Download:Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain IA [auth J] SDF format, chain Y [auth F] SDF format, chain W [auth E] SDF format, chain T [auth D] SDF format, chain S [auth C] SDF format, chain QA [auth L] SDF format, chain O [auth B] SDF format, chain NA [auth K] SDF format, chain M [auth A] SDF format, chain GA [auth I] SDF format, chain EA [auth H] MOL2 format, chain BA [auth G] MOL2 format, chain IA [auth J] MOL2 format, chain Y [auth F] MOL2 format, chain W [auth E] MOL2 format, chain T [auth D] MOL2 format, chain S [auth C] MOL2 format, chain QA [auth L] MOL2 format, chain O [auth B] MOL2 format, chain NA [auth K] MOL2 format, chain M [auth A] MOL2 format, chain GA [auth I] MOL2 format, chain EA [auth H] mmCIF format, chain BA [auth G] mmCIF format, chain IA [auth J] mmCIF format, chain Y [auth F] mmCIF format, chain W [auth E] mmCIF format, chain T [auth D] mmCIF format, chain S [auth C] mmCIF format, chain QA [auth L] mmCIF format, chain O [auth B] mmCIF format, chain NA [auth K] mmCIF format, chain M [auth A] mmCIF format, chain GA [auth I] mmCIF format, chain EA [auth H]	BA [auth G] EA [auth H] GA [auth I] IA [auth J] M [auth A] BA [auth G], EA [auth H], GA [auth I], IA [auth J], M [auth A], NA [auth K], O [auth B], QA [auth L], S [auth C], T [auth D], W [auth E], Y [auth F]	(1S,4S,5S)-1,4,5-TRIHYDROXY-3-[3-(PHENYLTHIO)PHENYL]CYCLOHEX-2-ENE-1-CARBOXYLIC ACID C₁₉ H₁₈ O₅ S QMNMNSINKIFYBV-LMMKCTJWSA-N		Interactions Focus chain BA [auth G] Focus chain EA [auth H] Focus chain GA [auth I] Focus chain IA [auth J] Focus chain M [auth A] Focus chain NA [auth K] Focus chain O [auth B] Focus chain QA [auth L] Focus chain S [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Y [auth F] Interactions & Density Focus chain BA [auth G] Focus chain EA [auth H] Focus chain GA [auth I] Focus chain IA [auth J] Focus chain M [auth A] Focus chain NA [auth K] Focus chain O [auth B] Focus chain QA [auth L] Focus chain S [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Y [auth F]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain U [auth D] SDF format, chain KA [auth J] SDF format, chain HA [auth I] MOL2 format, chain Q [auth B] MOL2 format, chain U [auth D] MOL2 format, chain KA [auth J] MOL2 format, chain HA [auth I] mmCIF format, chain Q [auth B] mmCIF format, chain U [auth D] mmCIF format, chain KA [auth J] mmCIF format, chain HA [auth I]	HA [auth I], KA [auth J], Q [auth B], U [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain HA [auth I] Focus chain KA [auth J] Focus chain Q [auth B] Focus chain U [auth D] Interactions & Density Focus chain HA [auth I] Focus chain KA [auth J] Focus chain Q [auth B] Focus chain U [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain P [auth B] SDF format, chain JA [auth J] SDF format, chain CA [auth G] MOL2 format, chain Z [auth F] MOL2 format, chain P [auth B] MOL2 format, chain JA [auth J] MOL2 format, chain CA [auth G] mmCIF format, chain Z [auth F] mmCIF format, chain P [auth B] mmCIF format, chain JA [auth J] mmCIF format, chain CA [auth G]	CA [auth G], JA [auth J], P [auth B], Z [auth F]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain CA [auth G] Focus chain JA [auth J] Focus chain P [auth B] Focus chain Z [auth F] Interactions & Density Focus chain CA [auth G] Focus chain JA [auth J] Focus chain P [auth B] Focus chain Z [auth F]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain PA [auth K] SDF format, chain R [auth B] SDF format, chain X [auth E] SDF format, chain V [auth D] SDF format, chain RA [auth L] SDF format, chain OA [auth K] SDF format, chain N [auth A] SDF format, chain MA [auth J] SDF format, chain LA [auth J] SDF format, chain FA [auth H] SDF format, chain DA [auth G] SDF format, chain AA [auth F] MOL2 format, chain PA [auth K] MOL2 format, chain R [auth B] MOL2 format, chain X [auth E] MOL2 format, chain V [auth D] MOL2 format, chain RA [auth L] MOL2 format, chain OA [auth K] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth J] MOL2 format, chain LA [auth J] MOL2 format, chain FA [auth H] MOL2 format, chain DA [auth G] MOL2 format, chain AA [auth F] mmCIF format, chain PA [auth K] mmCIF format, chain R [auth B] mmCIF format, chain X [auth E] mmCIF format, chain V [auth D] mmCIF format, chain RA [auth L] mmCIF format, chain OA [auth K] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth J] mmCIF format, chain LA [auth J] mmCIF format, chain FA [auth H] mmCIF format, chain DA [auth G] mmCIF format, chain AA [auth F]	AA [auth F] DA [auth G] FA [auth H] LA [auth J] MA [auth J] AA [auth F], DA [auth G], FA [auth H], LA [auth J], MA [auth J], N [auth A], OA [auth K], PA [auth K], R [auth B], RA [auth L], V [auth D], X [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain LA [auth J] Focus chain MA [auth J] Focus chain N [auth A] Focus chain OA [auth K] Focus chain PA [auth K] Focus chain R [auth B] Focus chain RA [auth L] Focus chain V [auth D] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain LA [auth J] Focus chain MA [auth J] Focus chain N [auth A] Focus chain OA [auth K] Focus chain PA [auth K] Focus chain R [auth B] Focus chain RA [auth L] Focus chain V [auth D] Focus chain X [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.334 (Depositor), 0.301 (DCC)
R-Value Work: 0.274 (Depositor), 0.298 (DCC)
R-Value Observed: 0.277 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 195.755	α = 65.84
b = 195.73	β = 65.89
c = 239.68	γ = 89.97

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-04-10

Deposition Author(s):

Payne, R.J.

Riboldi-Tunnicliffe, A.

Abell, A.D.

Lapthorn, A.J.

Abell, C.

Revision History (Full details and data files)

Version 1.0: 2007-04-10
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-05-08
Changes: Data collection, Database references, Experimental preparation, Other
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description