1PXX

CRYSTAL STRUCTURE OF DICLOFENAC BOUND TO THE CYCLOOXYGENASE ACTIVE SITE OF COX-2

PDB DOI: https://doi.org/10.2210/pdb1PXX/pdb

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

Deposited: 2003-07-07 Released: 2003-09-09
Deposition Author(s): Kiefer, J.R., Rowlinson, S.W., Prusakiewicz, J.J., Pawlitz, J.L., Kozak, K.R., Kalgutkar, A.S., Stallings, W.C., Marnett, L.J., Kurumbail, R.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.302
R-Value Work: 0.254

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 284.89 kDa
Atom Count: 18,778
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 OR COX2 OR COX-2 OR TIS10 OR PGHS-B 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

Help

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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H	3		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: G47362BJ GlyCosmos: G47362BJ GlyGen: G47362BJ

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain Y [auth D] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D]	L [auth A], P [auth B], T [auth C], Y [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain L [auth A] Focus chain P [auth B] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain L [auth A] Focus chain P [auth B] Focus chain T [auth C] Focus chain Y [auth D]
DIF Query on DIF Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain Q [auth B] SDF format, chain U [auth C] SDF format, chain Z [auth D] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Z [auth D]	M [auth A], Q [auth B], U [auth C], Z [auth D]	2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID C₁₄ H₁₁ Cl₂ N O₂ DCOPUUMXTXDBNB-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain Q [auth B] Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain M [auth A] Focus chain Q [auth B] Focus chain U [auth C] Focus chain Z [auth D]
BOG Query on BOG Download Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain K [auth A] MOL2 format, chain X [auth D] MOL2 format, chain K [auth A]	K [auth A], X [auth D]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain K [auth A] Focus chain X [auth D] Interactions & Density Focus chain K [auth A] Focus chain X [auth D]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain I [auth A]	I [auth A] J [auth A] N [auth B] O [auth B] R [auth C] I [auth A], J [auth A], N [auth B], O [auth B], R [auth C], S [auth C], V [auth D], W [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
DIF	BindingDB: 1PXX	IC50: min: 5, max: 2.36e+4 (nM) from 22 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900017 Query on PRD_900017	E, F, G, H	triacetyl-beta-chitotriose	Oligosaccharide / Inhibitor		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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.302
R-Value Work: 0.254
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.145	α = 90
b = 135.09	β = 90
c = 124.165	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2003-09-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-09-09
Type: Initial release
Version 1.1: 2007-10-16
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary