	235,183 Structures from the PDB
	1,068,577 Computed Structure Models (CSM)

2P95|pdb_00002p95

Factor xa in complex with the inhibitor 5-chloro-N-((1R,2S)-2-(4-(2-oxopyridin-1(2H)-YL)benzamido) cyclopentyl)thiophene-2-carboxamide

PDB DOI: https://doi.org/10.2210/pdb2P95/pdb

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

Deposited: 2007-03-23 Released: 2007-07-24
Deposition Author(s): Chang, C.-H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.271 (Depositor), 0.264 (DCC)
R-Value Work:
0.239 (Depositor), 0.229 (DCC)
R-Value Observed:
0.241 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

SAR and X-ray structures of enantiopure 1,2-cis-(1R,2S)-cyclopentyldiamine and cyclohexyldiamine derivatives as inhibitors of coagulation Factor Xa

Qiao, J.X., Chang, C.-H., Cheney, D.L., Morin, P.E., Wang, G.Z., King, S.R., Wang, T.C., Rendina, A.R., Luettgen, J.M., Knabb, R.M., Wexler, R.R., Lam, P.Y.S.

(2007) Bioorg Med Chem Lett 17: 4419-4427

PubMed: 17588746 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2007.06.029
Primary Citation of Related Structures:
2P93,2P94,2P95

PubMed Abstract:
In the search of Factor Xa (FXa) inhibitors structurally different from the pyrazole-based series, we identified a viable series of enantiopure cis-(1R,2S)-cycloalkyldiamine derivatives as potent and selective inhibitors of FXa. Among them, cyclohexyldiamide 7 and cyclopentyldiamide 9 were the most potent neutral compounds, and had good anticoagulant activity comparable to the pyrazole-based analogs. Crystal structures of 7-FXa and 9-FXa illustrate binding similarities and differences between the five- and the six-membered core systems, and provide rationales for the observed SAR of P1 and linker moieties.

Organizational Affiliation

Bristol-Myers Squibb Company, Research and Development, PO Box 5400, Princeton, NJ 08543-5400, USA. jennifer.qiao@bms.com

Macromolecule Content

Total Structure Weight: 32.48 kDa
Atom Count: 2,356
Modelled Residue Count: 286
Deposited Residue Count: 286
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Factor Xa	A	234	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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Factor Xa	B [auth L]	52	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ME5 Query on ME5 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	5-CHLORO-N-((1R,2S)-2-(4-(2-OXOPYRIDIN-1(2H)-YL)BENZAMIDO) CYCLOPENTYL)THIOPHENE-2-CARBOXAMIDE C₂₂ H₂₀ Cl N₃ O₃ S QCPYHSAHOYXXQK-DLBZAZTESA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
ME5	BindingDB: 2P95	Ki: 0.43 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.271 (Depositor), 0.264 (DCC)
R-Value Work: 0.239 (Depositor), 0.229 (DCC)
R-Value Observed: 0.241 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.6	α = 90
b = 72.3	β = 90
c = 78.9	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
EPMR	phasing
CNX	refinement

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-07-24

Deposition Author(s):

Chang, C.-H.

Revision History (Full details and data files)

Version 1.0: 2007-07-24
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Advisory, Refinement description
Version 1.4: 2024-10-09
Changes: Advisory, Data collection, Database references, Structure summary