2VWN

Aminopyrrolidine Factor Xa inhibitor

PDB DOI: https://doi.org/10.2210/pdb2VWN/pdb

Classification: BLOOD CLOTTING
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2008-06-26 Released: 2009-07-07
Deposition Author(s): Groebke-Zbinden, K., Banner, D.W., Benz, J.M., Blasco, F., Decoret, G., Himber, J., Kuhn, B., Panday, N., Ricklin, F., Risch, P., Schlatter, D., Stahl, M., Unger, R., Haap, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free: 0.228
R-Value Work: 0.191
R-Value Observed: 0.193

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Design of Novel Aminopyrrolidine Factor Xa Inhibitors from a Screening Hit.

Zbinden, K.G., Anselm, L., Banner, D.W., Benz, J.M., Blasco, F., Decoret, G., Himber, J., Kuhn, B., Panday, N., Ricklin, F., Risch, P., Schlatter, D., Stahl, M., Thomi, S., Unger, R., Haap, W.

(2009) Eur J Med Chem 44: 2787

PubMed: 19200624 Search on PubMed
DOI: https://doi.org/10.1016/j.ejmech.2008.12.025
Primary Citation of Related Structures:
2VVC, 2VVU, 2VVV, 2VWL, 2VWM, 2VWN, 2VWO

PubMed Abstract:
Starting from a hit identified by focused screening, 3-aminopyrrolidine factor Xa inhibitors were designed. The binding mode as determined by X-ray structural analysis as well as the pharmacokinetic behaviour of selected compounds is discussed.

Organizational Affiliation

F Hoffmann - La Roche Ltd, Basel, Switzerland. katrin.groebke_zbinden@roche.com

Macromolecule Content

Total Structure Weight: 33.88 kDa
Atom Count: 2,523
Modelled Residue Count: 280
Deposited Residue Count: 296
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACTIVATED FACTOR XA HEAVY CHAIN	A	241	Homo sapiens	Mutation(s): 1 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 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00742
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
H25 Query on H25 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-thiophene-2-carboxylic acid ((3S,4S)-1-{[2-fluoro-4-(2-oxo-2H-pyridin-1-yl)-phenylcarbamoyl]-methyl}-4-hydroxy-pyrrolidin-3-yl)-amide C₂₂ H₂₀ Cl F N₄ O₄ S ARAVOODWJJJNBY-IRXDYDNUSA-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]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth A]	E [auth A], H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth A] Interactions & Density Focus chain E [auth A] Focus chain H [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
H25	PDBBind: 2VWN	Ki: 10 (nM) from 1 assay(s)
H25	BindingDB: 2VWN	Ki: 10 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free: 0.228
R-Value Work: 0.191
R-Value Observed: 0.193
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.54	α = 90
b = 105.54	β = 90
c = 49.79	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-07-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-07-07
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: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.4: 2024-11-13
Changes: Structure summary