2FLB | pdb_00002flb

Discovery of a Novel Hydroxy Pyrazole Based Factor IXa Inhibitor

PDB DOI: https://doi.org/10.2210/pdb2FLB/pdb

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

Deposited: 2006-01-05 Released: 2006-04-04
Deposition Author(s): Katz, B.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.280 (Depositor)
R-Value Work:
0.247 (Depositor), 0.236 (DCC)
R-Value Observed:
0.250 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Discovery of novel hydroxy pyrazole based factor IXa inhibitor.

Vijaykumar, D., Sprengeler, P.A., Shaghafi, M., Spencer, J.R., Katz, B.A., Yu, C., Rai, R., Young, W.B., Schultz, B., Janc, J.

(2006) Bioorg Med Chem Lett 16: 2796-2799

PubMed: 16487703 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2006.01.123
Primary Citation Related Structures:
2FLB

PubMed Abstract:
Synthesis and biological data of a novel selective and efficacious factor IXa inhibitor are described along with its crystal structure in factor VIIa.

Organizational Affiliation

Celera, 180 Kimball Way, South San Francisco, CA 94080, USA. dvijayku@hotmail.com

Macromolecule Content

Total Structure Weight: 70.21 kDa
Atom Count: 4,278
Modeled Residue Count: 501
Deposited Residue Count: 624
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII	A [auth L]	152	Homo sapiens	Mutation(s): 0 Gene Names: F7 EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens) Explore P08709 Go to UniProtKB: P08709
PHAROS: P08709 GTEx: ENSG00000057593
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08709
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII	B [auth H]	254	Homo sapiens	Mutation(s): 0 Gene Names: F7 EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens) Explore P08709 Go to UniProtKB: P08709
PHAROS: P08709 GTEx: ENSG00000057593
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08709
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tissue factor	C [auth T]	218	Homo sapiens	Mutation(s): 0 Gene Names: F3
UniProt & NIH Common Fund Data Resources
Find proteins for P13726 (Homo sapiens) Explore P13726 Go to UniProtKB: P13726
PHAROS: P13726 GTEx: ENSG00000117525
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13726
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6NH Query on 6NH Download:Ideal Coordinates CCD File SDF format, chain D [auth H] MOL2 format, chain D [auth H] mmCIF format, chain D [auth H]	D [auth H]	2-(4-HYDROXY-5-PHENYL-1H-PYRAZOL-3-YL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE C₁₇ H₁₄ N₆ O CKSIVONWCYACAP-UHFFFAOYSA-N		Interactions Focus chain D [auth H] Interactions & Density Focus chain D [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.280 (Depositor)
R-Value Work: 0.247 (Depositor), 0.236 (DCC)
R-Value Observed: 0.250 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.45	α = 90
b = 69.03	β = 90.21
c = 78.76	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-04-04

Deposition Author(s):

Katz, B.A.

Revision History (Full details and data files)

Version 1.0: 2006-04-04
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: 2017-10-11
Changes: Data collection, Refinement description
Version 1.4: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary