2XBY | pdb_00002xby

Factor Xa in complex with a pyrrolidine-3,4-dicarboxylic acid inhibitor

PDB DOI: https://doi.org/10.2210/pdb2XBY/pdb

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

Deposited: 2010-04-15 Released: 2010-08-04
Deposition Author(s): Banner, D.W., Benz, J., Schlatter, D., Thomi, S., Haap, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free:
0.246 (Depositor), 0.210 (DCC)
R-Value Work:
0.210 (Depositor), 0.208 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: other
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Discovery of a Factor Xa Inhibitor (3R,4R)-1-(2,2-Difluoro-Ethyl)-Pyrrolidine-3,4-Dicarboxylic Acid 3-[(5-Chloro-Pyridin-2-Yl)-Amide] 4-{[2-Fluoro-4-(2-Oxo-2H-Pyridin-1-Yl)-Phenyl]-Amide} as a Clinical Candidate.

Anselm, L., Banner, D.W., Benz, J., Groebke Zbinden, K., Himber, J., Hilpert, H., Huber, W., Kuhn, B., Mary, J.L., Otteneder, M.B., Panday, N., Ricklin, F., Stahl, M., Thomi, S., Haap, W.

(2010) Bioorg Med Chem 20: 5313

PubMed: 20650636 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2010.06.126
Primary Citation Related Structures:
2XBV, 2XBW, 2XBX, 2XBY, 2XC0, 2XC4, 2XC5

PubMed Abstract:
A series of (3R,4R)-pyrrolidine-3,4-dicarboxylic acid amides was investigated with respect to their factor Xa inhibitory activity, selectivity, pharmacokinetic properties, and ex vivo antithrombotic activity. The clinical candidate from this series, R1663, exhibits excellent selectivity against a panel of serine proteases and good pharmacokinetic properties in rats and monkeys. A Phase I clinical study with R1663 has been finalized.

Organizational Affiliation

F. Hoffmann-La Roche Ltd, Pharma Research, Basel, Switzerland.

Macromolecule Content

Total Structure Weight: 33.85 kDa
Atom Count: 2,426
Modeled Residue Count: 279
Deposited Residue Count: 296
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACTIVATED FACTOR XA HEAVY CHAIN	A	241	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% 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
FACTOR X LIGHT CHAIN	B [auth L]	55	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00742
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
63C Query on 63C 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]	(3R,4R)-1-METHYLCARBAMOYLMETHYL-PYRROLIDINE-3,4-DICARBOXYLIC ACID 3-[(4-CHLORO-PHENYL)-AMIDE] 4-{[2-FLUORO-4-(2-OXO-2H-PYRIDIN-1-YL)-PHENYL]-AMIDE} C₂₆ H₂₅ Cl F N₅ O₄ DXHIEYAKKGEXDY-PMACEKPBSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CA Query on CA 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]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.246 (Depositor), 0.210 (DCC)
R-Value Work: 0.210 (Depositor), 0.208 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.64	α = 90
b = 106.64	β = 90
c = 50.9	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-08-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-08-04
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-06-28
Changes: Data collection
Version 1.4: 2024-05-01
Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.5: 2024-11-06
Changes: Structure summary