4FM5

X-ray structure of des-methylflurbiprofen bound to murine COX-2

PDB DOI: https://doi.org/10.2210/pdb4FM5/pdb

Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Organism(s): Mus musculus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2012-06-15 Released: 2012-08-29
Deposition Author(s): Xu, S., Banerjee, S., Windsor, M.A., Marnett, L.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free: 0.290
R-Value Work: 0.240
R-Value Observed: 0.243

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 283.21 kDa
Atom Count: 18,554
Modelled Residue Count: 2,208
Deposited Residue Count: 2,416
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prostaglandin G/H synthase 2	A, B, C, D	604	Mus musculus	Mutation(s): 0 Gene Names: Ptgs2, Cox-2, Cox2, Pghs-b, Tis10 EC: 1.14.99.1
UniProt
Find proteins for Q05769 (Mus musculus) Explore Q05769 Go to UniProtKB: Q05769
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q05769
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H	2		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain U [auth D] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D]	K [auth A], N [auth B], R [auth C], U [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain K [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain U [auth D] Interactions & Density Focus chain K [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain U [auth D]
BOG Query on BOG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth D] SDF format, chain J [auth A] SDF format, chain P [auth C] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] MOL2 format, chain J [auth A] MOL2 format, chain P [auth C]	I [auth A] J [auth A] M [auth B] P [auth C] Q [auth C] I [auth A], J [auth A], M [auth B], P [auth C], Q [auth C], T [auth D]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D]
DF0 Query on DF0 Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain V [auth D] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D]	L [auth A], O [auth B], S [auth C], V [auth D]	(2-fluorobiphenyl-4-yl)acetic acid C₁₄ H₁₁ F O₂ ZLLZRKQQNGBXRD-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain O [auth B] Focus chain S [auth C] Focus chain V [auth D] Interactions & Density Focus chain L [auth A] Focus chain O [auth B] Focus chain S [auth C] Focus chain V [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
DF0	BindingDB: 4FM5	IC50: min: 110, max: 600 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free: 0.290
R-Value Work: 0.240
R-Value Observed: 0.243
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.632	α = 90
b = 135.696	β = 90
c = 125.15	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-08-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-08-29
Type: Initial release
Version 1.1: 2012-12-19
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

4FM5

X-ray structure of des-methylflurbiprofen bound to murine COX-2

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)