4A7I

Factor Xa in complex with a potent 2-amino-ethane sulfonamide inhibitor

PDB DOI: https://doi.org/10.2210/pdb4A7I/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2011-11-14 Released: 2012-02-01
Deposition Author(s): Nazare, M., Matter, H., Will, D.W., Wagner, M., Urmann, M., Czech, J., Schreuder, H., Bauer, A., Ritter, K., Wehner, V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.253
R-Value Work: 0.198
R-Value Observed: 0.198

Starting Model: other
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Fragment Deconstruction of Small, Potent Factor Xa Inhibitors: Exploring the Superadditivity Energetics of Fragment Linking in Protein-Ligand Complexes.

Nazare, M., Matter, H., Will, D.W., Wagner, M., Urmann, M., Czech, J., Schreuder, H., Bauer, A., Ritter, K., Wehner, V.

(2012) Angew Chem Int Ed Engl 51: 905

PubMed: 22190348 Search on PubMed
DOI: https://doi.org/10.1002/anie.201107091
Primary Citation of Related Structures:
4A7I

Organizational Affiliation

Sanofi-Aventis Deutschland GmbH, R&D, Industriepark Höchst, Building G878, 65926 Frankfurt am Main, Germany. marc.nazare@sanofi-aventis.com

Macromolecule Content

Total Structure Weight: 39.52 kDa
Atom Count: 2,478
Modelled Residue Count: 287
Deposited Residue Count: 350
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FACTOR X LIGHT CHAIN	A	96	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
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
ACTIVATED FACTOR XA HEAVY CHAIN XA	B	254	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
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
A7I Query on A7I Download Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B]	D [auth B]	5-CHLORO-THIOPHENE-2-CARBOXYLIC ACID [2-(1--ISOPROPYL-PIPERIDIN-4-YLSULFAMOYL)-ETHYL]-AMIDE C₁₅ H₂₄ Cl N₃ O₃ S₂ XIOBNAKYNXSFFO-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B]	C [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
A7I	PDBBind: 4A7I	Ki: 2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.253
R-Value Work: 0.198
R-Value Observed: 0.198
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.253	α = 90
b = 72.042	β = 90
c = 77.416	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XSCALE	data scaling
CNX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-02-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-02-01
Type: Initial release
Version 1.1: 2024-05-01
Changes: Data collection, Database references, Derived calculations, Other, Refinement description