3NTG | pdb_00003ntg

Crystal structure of COX-2 with selective compound 23d-(R)

PDB DOI: https://doi.org/10.2210/pdb3NTG/pdb

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

Deposited: 2010-07-04 Released: 2010-10-27
Deposition Author(s): Wang, J.L., Limburg, D., Graneto, M.J., Carter, J.C., Talley, J.J., Kiefer, J.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free:
0.255 (Depositor), 0.234 (DCC)
R-Value Work:
0.206 (Depositor)
R-Value Observed:
0.211 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

The novel benzopyran class of selective cyclooxygenase-2 inhibitors. Part 2: The second clinical candidate having a shorter and favorable human half-life.

Wang, J.L., Limburg, D., Graneto, M.J., Springer, J., Hamper, J.R., Liao, S., Pawlitz, J.L., Kurumbail, R.G., Maziasz, T., Talley, J.J., Kiefer, J.R., Carter, J.

(2010) Bioorg Med Chem Lett 20: 7159-7163

PubMed: 20709553 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2010.07.054
Primary Citation Related Structures:
3LN0, 3LN1, 3MQE, 3NTG

PubMed Abstract:
In this Letter, we provide the structure-activity relationships, optimization of design, testing criteria, and human half-life data for a series of selective COX-2 inhibitors. During the course of our structure-based drug design efforts, we discovered two distinct binding modes within the COX-2 active site for differently substituted members of this class. The challenge of a undesirably long human half-life for the first clinical candidate 1t(1/2)=360 h was addressed by multiple strategies, leading to the discovery of 29b-(S) (SC-75416) with t(1/2)=34 h.

Organizational Affiliation

Pfizer Global Research and Development, Chesterfield, MO 63017, USA. jl47wang@yahoo.com

Macromolecule Content

Total Structure Weight: 261.16 kDa
Atom Count: 19,469
Modeled Residue Count: 2,208
Deposited Residue Count: 2,208
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prostaglandin G/H synthase 2	A, B, C, D	552	Mus musculus	Mutation(s): 0 Gene Names: Cox-2, Cox2, mCG_5001, Pghs-b, Ptgs2, Tis10 EC: 1.14.99.1
UniProt
Find proteins for Q05769 (Mus musculus) Explore Q05769 Go to UniProtKB: Q05769
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q05769
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: Q05769-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain S [auth D] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D]	I [auth A], M [auth B], P [auth C], S [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain I [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Interactions & Density Focus chain I [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D]
D72 Query on D72 Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain R [auth C] SDF format, chain O [auth B] SDF format, chain L [auth A] MOL2 format, chain V [auth D] MOL2 format, chain R [auth C] MOL2 format, chain O [auth B] MOL2 format, chain L [auth A] mmCIF format, chain V [auth D] mmCIF format, chain R [auth C] mmCIF format, chain O [auth B] mmCIF format, chain L [auth A]	L [auth A], O [auth B], R [auth C], V [auth D]	(2R)-6,8-dichloro-7-(2-methylpropoxy)-2-(trifluoromethyl)-2H-chromene-3-carboxylic acid C₁₅ H₁₃ Cl₂ F₃ O₄ FQKMILFVTQADHR-CYBMUJFWSA-N		Interactions Focus chain L [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain V [auth D] Interactions & Density Focus chain L [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain V [auth D]
BOG Query on BOG Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain U [auth D] MOL2 format, chain K [auth A] MOL2 format, chain U [auth D] mmCIF format, chain K [auth A] mmCIF format, chain U [auth D]	K [auth A], U [auth D]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain K [auth A] Focus chain U [auth D] Interactions & Density Focus chain K [auth A] Focus chain U [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 T [auth D] SDF format, chain Q [auth C] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain T [auth D] MOL2 format, chain Q [auth C] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain T [auth D] mmCIF format, chain Q [auth C]	J [auth A], N [auth B], Q [auth C], T [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D] Interactions & Density Focus chain J [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.255 (Depositor), 0.234 (DCC)
R-Value Work: 0.206 (Depositor)
R-Value Observed: 0.211 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.268	α = 90
b = 134.273	β = 90
c = 122.615	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-10-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-10-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-12-27
Changes: Data collection, Database references, Structure summary
Version 2.2: 2024-11-20
Changes: Structure summary

3NTG | pdb_00003ntg

Crystal structure of COX-2 with selective compound 23d-(R)

Literature

The novel benzopyran class of selective cyclooxygenase-2 inhibitors. Part 2: The second clinical candidate having a shorter and favorable human half-life.

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

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