4FGL | pdb_00004fgl

Reduced quinone reductase 2 in complex with chloroquine

PDB DOI: https://doi.org/10.2210/pdb4FGL/pdb

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

Deposited: 2012-06-04 Released: 2013-03-13
Deposition Author(s): Leung, K.K., Shilton, B.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.173 (Depositor), 0.173 (DCC)
R-Value Work:
0.159 (Depositor), 0.157 (DCC)
R-Value Observed:
0.160 (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 structures of quinone reductase 2 bound to antimalarial drugs reveal conformational change upon reduction

Leung, K.K., Shilton, B.H.

(2013) J Biological Chem

Macromolecule Content

Total Structure Weight: 109.44 kDa
Atom Count: 8,748
Modeled Residue Count: 923
Deposited Residue Count: 932
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosyldihydronicotinamide dehydrogenase [quinone]	A, B, C, D	233	Homo sapiens	Mutation(s): 0 Gene Names: NMOR2, NQO2 EC: 1.10.99.2 (PDB Primary Data), 1.10.5.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P16083 (Homo sapiens) Explore P16083 Go to UniProtKB: P16083
PHAROS: P16083 GTEx: ENSG00000124588
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P16083
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D]	F [auth A], I [auth B], L [auth C], O [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]
CLQ Query on CLQ Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain M [auth C] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain M [auth C] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain M [auth C]	G [auth A], J [auth B], M [auth C], P [auth D], Q [auth D]	N4-(7-CHLORO-QUINOLIN-4-YL)-N1,N1-DIETHYL-PENTANE-1,4-DIAMINE C₁₈ H₂₆ Cl N₃ WHTVZRBIWZFKQO-CQSZACIVSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D] mmCIF format, chain E [auth A]	E [auth A], H [auth B], K [auth C], N [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
CLQ	BindingDB: 4FGL	IC50: 1500 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.173 (Depositor), 0.173 (DCC)
R-Value Work: 0.159 (Depositor), 0.157 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.31	α = 90
b = 105.71	β = 90.17
c = 82	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MxDC	data collection
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-03-13

Deposition Author(s):

Leung, K.K.

Shilton, B.H.

Revision History (Full details and data files)

Version 1.0: 2013-03-13
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

4FGL | pdb_00004fgl

Reduced quinone reductase 2 in complex with chloroquine

Literature

Crystal structures of quinone reductase 2 bound to antimalarial drugs reveal conformational change upon reduction

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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