2F9B

Discovery of Novel Heterocyclic Factor VIIa Inhibitors

PDB DOI: https://doi.org/10.2210/pdb2F9B/pdb

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

Deposited: 2005-12-05 Released: 2006-02-28
Deposition Author(s): Rai, R., Kolesnikov, A., Sprengeler, P.A., Torkelson, S., Ton, T., Katz, B.A., Yu, C., Hendrix, J., Shrader, W.D., Stephens, R., Cabuslay, R., Sanford, E., Young, W.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.54 Å
R-Value Free: 0.286
R-Value Work: 0.226
R-Value Observed: 0.230

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Discovery of novel heterocyclic factor VIIa inhibitors.

Rai, R., Kolesnikov, A., Sprengeler, P.A., Torkelson, S., Ton, T., Katz, B.A., Yu, C., Hendrix, J., Shrader, W.D., Stephens, R., Cabuslay, R., Sanford, E., Young, W.B.

(2006) Bioorg Med Chem Lett 16: 2270-2273

PubMed: 16460932 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2006.01.017
Primary Citation of Related Structures:
2F9B

PubMed Abstract:
Structure-activity relationships and binding mode of novel heterocyclic factor VIIa inhibitors will be described. In these inhibitors, a highly basic 5-amidinoindole moiety has been successfully replaced with a less basic 5-aminopyrrolo[3,2-b]pyridine scaffold.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 70.29 kDa
Atom Count: 4,059
Modelled Residue Count: 497
Deposited Residue Count: 624
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08709
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08709
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13726
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
N1H Query on N1H 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]	{5-(5-AMINO-1H-PYRROLO[3,2-B]PYRIDIN-2-YL)-6-HYDROXY-3'-NITRO-BIPHENYL-3-YL]-ACETIC ACID C₂₁ H₁₆ N₄ O₅ BVBGZXXLVHYBKI-UHFFFAOYSA-N		Interactions Focus chain D [auth H] Interactions & Density Focus chain D [auth H]

Binding Affinity Annotations
ID	Source	Binding Affinity
N1H	PDBBind: 2F9B	Ki: 300 (nM) from 1 assay(s)
N1H	BindingDB: 2F9B	Ki: 300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.54 Å
R-Value Free: 0.286
R-Value Work: 0.226
R-Value Observed: 0.230
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.07	α = 90
b = 68.94	β = 90.17
c = 78.73	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
XTALVIEW	refinement
X-PLOR	refinement
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-02-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-02-28
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: Refinement description
Version 1.4: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2024-10-16
Changes: Structure summary