3NFR | pdb_00003nfr

Casimiroin analog inhibitor of quinone reductase 2

PDB DOI: https://doi.org/10.2210/pdb3NFR/pdb

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

Deposited: 2010-06-10 Released: 2012-01-11
Deposition Author(s): Sturdy, M., Mesecar, A.D., Jermihov, K., Cushman, M., Maiti, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free:
0.219 (Depositor), 0.223 (DCC)
R-Value Work:
0.194 (Depositor)
R-Value Observed:
0.196 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

X-ray Crystallographic Structure Activity Relationship (SAR) of Casimiroin and its Analogs Bound to Human Quinone Reductase 2

Sturdy, M., Maiti, A., Jermihov, K., Cushman, M., Mesecar, A.D.

To be published.

Macromolecule Content

Total Structure Weight: 53.87 kDa
Atom Count: 4,086
Modeled Residue Count: 460
Deposited Residue Count: 460
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosyldihydronicotinamide dehydrogenase [quinone]	A, B	230	Homo sapiens	Mutation(s): 0 Gene Names: NQO2, NMOR2 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 H [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
EWQ Query on EWQ Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	6,8-dimethoxy-1,4-dimethylquinolin-2(1H)-one C₁₃ H₁₅ N O₃ BYYQQWLTZFBHIQ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
EWQ	BindingDB: 3NFR	IC50: 1900 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free: 0.219 (Depositor), 0.223 (DCC)
R-Value Work: 0.194 (Depositor)
R-Value Observed: 0.196 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.057	α = 90
b = 83.206	β = 90
c = 106.465	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-01-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-01-11
Type: Initial release
Version 1.1: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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