4QQE | pdb_00004qqe

Crystal structure of WDR5, WD repeat domain 5 in complex with compound SGC-DS-MT-0345

PDB DOI: https://doi.org/10.2210/pdb4QQE/pdb

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

Deposited: 2014-06-27 Released: 2014-07-30
Deposition Author(s): Dong, A., Dombrovski, L., Wernimont, A., Smil, D., Getlik, M., Senisterra, G., Poda, G., Al-Awar, R., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Brown, P.J., Schapira, M., Vedadi, M., Wu, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.218 (Depositor), 0.220 (DCC)
R-Value Work:
0.173 (Depositor), 0.180 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of WDR5, WD repeat domain 5 in complex with compound SGC-DS-MT-0345

Dombrovski, L., Dong, A., Wernimont, A., Smil, D., Getlik, M., Senisterra, G., Poda, G., Al-Awar, R., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Brown, P.J., Schapira, M., Vedadi, M., Wu, H.

To be published.

Macromolecule Content

Total Structure Weight: 35.02 kDa
Atom Count: 2,634
Modelled Residue Count: 304
Deposited Residue Count: 312
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WD repeat-containing protein 5	A	312	Homo sapiens	Mutation(s): 0 Gene Names: BIG3, WDR5
UniProt & NIH Common Fund Data Resources
Find proteins for P61964 (Homo sapiens) Explore P61964 Go to UniProtKB: P61964
PHAROS: P61964 GTEx: ENSG00000196363
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61964
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
37F Query on 37F Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	N-[2-(4-methylpiperazin-1-yl)-5-(quinolin-3-yl)phenyl]-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide C₂₇ H₂₄ F₃ N₅ O₂ BHSUCGLRVZHATB-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
37F	BindingDB: 4QQE	Kd: 50 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.218 (Depositor), 0.220 (DCC)
R-Value Work: 0.173 (Depositor), 0.180 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.896	α = 90
b = 85.267	β = 90
c = 40.209	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-07-30

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2014-07-30
Type: Initial release
Version 1.1: 2014-10-15
Changes: Database references, Source and taxonomy
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description