6Z52 | pdb_00006z52

Crystal structure of CLK3 in complex with macrocycle ODS2003136

PDB DOI: https://doi.org/10.2210/pdb6Z52/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-05-26 Released: 2020-06-03
Deposition Author(s): Chaikuad, A., Benderitter, P., Hoflack, J., Denis, A., Knapp, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.230 (Depositor), 0.233 (DCC)
R-Value Work:
0.178 (Depositor), 0.185 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of CLK3 in complex with macrocycle ODS2003136

Chaikuad, A., Benderitter, P., Hoflack, J., Denis, A., Knapp, S., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 88.13 kDa
Atom Count: 6,635
Modeled Residue Count: 708
Deposited Residue Count: 720
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity protein kinase CLK3	A, B	360	Homo sapiens	Mutation(s): 0 Gene Names: CLK3 EC: 2.7.12.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49761 (Homo sapiens) Explore P49761 Go to UniProtKB: P49761
PHAROS: P49761 GTEx: ENSG00000179335
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49761
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Q8T (Subject of Investigation/LOI) Query on Q8T Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain FA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain FA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain FA [auth B]	FA [auth B], Q [auth A]	11,15-dimethyl-6-(4-methylpiperazin-1-yl)-8-oxa-2,11,15,19,21,23-hexazatetracyclo[15.6.1.13,7.020,24]pentacosa-1(23),3(25),4,6,17,20(24),21-heptaen-10-one C₂₅ H₃₄ N₈ O₂ SOJXCMRVYOLJEH-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Focus chain Q [auth A] Interactions & Density Focus chain FA [auth B] Focus chain Q [auth A]
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain Z [auth B] SDF format, chain X [auth B] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain CA [auth B] SDF format, chain BA [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain X [auth B] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain X [auth B] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], I [auth A], J [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], X [auth B], Z [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain X [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain X [auth B] Focus chain Z [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain T [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain T [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain W [auth B] SDF format, chain K [auth A] SDF format, chain H [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain W [auth B] MOL2 format, chain K [auth A] MOL2 format, chain H [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain W [auth B] mmCIF format, chain K [auth A] mmCIF format, chain H [auth A]	H [auth A], K [auth A], W [auth B], Y [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain K [auth A] Focus chain W [auth B] Focus chain Y [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth A] Focus chain W [auth B] Focus chain Y [auth B]