2PHB | pdb_00002phb

An Orally Efficacious Factor Xa Inhibitor

PDB DOI: https://doi.org/10.2210/pdb2PHB/pdb

Classification: BLOOD CLOTTING
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-04-10 Released: 2008-03-25
Deposition Author(s): Zhang, E., Kohrt, J.T., Bigge, C.F., Finzel, B.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.296 (Depositor), 0.279 (DCC)
R-Value Work:
0.260 (Depositor), 0.264 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The discovery of (2R,4R)-N-(4-chlorophenyl)-N- (2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl)-4-methoxypyrrolidine-1,2-dicarboxamide (PD 0348292), an orally efficacious factor Xa inhibitor

Kohrt, J.T., Bigge, C.F., Bryant, J.W., Casimiro-Garcia, A., Chi, L., Cody, W.L., Dahring, T., Dudley, D.A., Filipski, K.J., Haarer, S., Heemstra, R., Janiczek, N., Narasimhan, L., McClanahan, T., Peterson, J.T., Sahasrabudhe, V., Schaum, R., Van Huis, C.A., Welch, K.M., Zhang, E., Leadley, R.J., Edmunds, J.J.

(2007) Chem Biol Drug Des 70: 100-112

PubMed: 17683371 Search on PubMed
DOI: https://doi.org/10.1111/j.1747-0285.2007.00539.x
Primary Citation Related Structures:
2PHB

PubMed Abstract:
Herein, we report the discovery of novel, proline-based factor Xa inhibitors containing a neutral P1 chlorophenyl pharmacophore. Through the additional incorporation of 1-(4-amino-3-fluoro-phenyl)-1H-pyridin-2-one 22, as a P4 pharmacophore, we discovered compound 7 (PD 0348292). This compound is a selective, orally bioavailable, efficacious FXa inhibitor that is currently in phase II clinical trials for the treatment and prevention of thrombotic disorders.

Organizational Affiliation

Michigan Laboratories, Ann Arbor Campus, Pfizer Global Research and Development, 2800 Plymouth Road, Ann Arbor, MI 48105, USA. jeffrey.kohrt@pfizer.com

Macromolecule Content

Total Structure Weight: 32.43 kDa
Atom Count: 2,314
Modeled Residue Count: 285
Deposited Residue Count: 285
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor X, heavy chain	A	234	Homo sapiens	Mutation(s): 0 Gene Names: F10 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00742
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor X, light chain	B	51	Homo sapiens	Mutation(s): 0 Gene Names: F10 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00742
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
230 Query on 230 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	(2R,4R)-N~1~-(4-CHLOROPHENYL)-N~2~-[2-FLUORO-4-(2-OXOPYRIDIN-1(2H)-YL)PHENYL]-4-METHOXYPYRROLIDINE-1,2-DICARBOXAMIDE C₂₄ H₂₂ Cl F N₄ O₄ QQBKAVAGLMGMHI-WIYYLYMNSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CA Query on CA 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]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.296 (Depositor), 0.279 (DCC)
R-Value Work: 0.260 (Depositor), 0.264 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.483	α = 90
b = 72.406	β = 90
c = 77.715	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-03-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-03-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-18
Changes: Advisory, Refinement description
Version 1.3: 2024-11-06
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary