2P3U

Crystal structure of human factor XA complexed with 3-chloro-N-(4-chloro-2-{[(5-chloropyridin-2-yl)amino]carbonyl}-6-methoxyphenyl)-4-[(1-methyl-1H-imidazol-2-yl)methyl]thiophene-2-carboxamide {Pfizer 320663}

PDB DOI: https://doi.org/10.2210/pdb2P3U/pdb

Classification: BLOOD CLOTTING
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2007-03-09 Released: 2007-09-11
Deposition Author(s): Adler, M., Whitlow, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.210
R-Value Work: 0.191
R-Value Observed: 0.192

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Macromolecule Content

Total Structure Weight: 32.57 kDa
Atom Count: 2,524
Modelled Residue Count: 284
Deposited Residue Count: 285
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor X	A	52	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742 Go to UniProtKB: P00742
PHAROS: P00742 GTEx: ENSG00000126218
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00742
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor X	B	233	Homo sapiens	Mutation(s): 0 EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742 Go to UniProtKB: P00742
PHAROS: P00742 GTEx: ENSG00000126218
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00742
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
663 Query on 663 Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B]	E [auth B]	3-CHLORO-N-(4-CHLORO-2-{[(5-CHLOROPYRIDIN-2-YL)AMINO]CARBONYL}-6-METHOXYPHENYL)-4-[(1-METHYL-1H-IMIDAZOL-2-YL)METHYL]THIOPHENE-2-CARBOXAMIDE C₂₃ H₁₈ Cl₃ N₅ O₃ S WBFPCLIRIGEEBD-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B]	C [auth B], D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Interactions & Density Focus chain C [auth B] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.210
R-Value Work: 0.191
R-Value Observed: 0.192
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.014	α = 90
b = 71.717	β = 90
c = 78.651	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
Blu-Ice	data collection
MOSFLM	data reduction
SCALA	data scaling
X-PLOR	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-09-11

Deposition Author(s):

Adler, M.

Whitlow, M.

Revision History (Full details and data files)

Version 1.0: 2007-09-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

2P3U

Crystal structure of human factor XA complexed with 3-chloro-N-(4-chloro-2-{[(5-chloropyridin-2-yl)amino]carbonyl}-6-methoxyphenyl)-4-[(1-methyl-1H-imidazol-2-yl)methyl]thiophene-2-carboxamide {Pfizer 320663}

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2