2B7D | pdb_00002b7d

Factor VIIa Inhibitors: Chemical Optimization, Preclinical Pharmacokinetics, Pharmacodynamics, and Efficacy in a Baboon Thrombosis Model

PDB DOI: https://doi.org/10.2210/pdb2B7D/pdb

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

Deposited: 2005-10-04 Released: 2006-02-14
Deposition Author(s): Young, W.B., Mordenti, J., Torkelson, S., Shrader, W.D., Kolesnikov, A., Rai, R., Liu, L., Hu, H., Leahy, E.M., Green, M.J., Sprengeler, P.A., Katz, B.A., Yu, C., Janc, J.W., Elrod, K.C., Marzec, U.M., Hanson, S.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free:
0.289 (Depositor), 0.240 (DCC)
R-Value Work:
0.247 (Depositor), 0.240 (DCC)
R-Value Observed:
0.250 (Depositor)

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

Factor VIIa inhibitors: Chemical optimization, preclinical pharmacokinetics, pharmacodynamics, and efficacy in an arterial baboon thrombosis model.

Young, W.B., Mordenti, J., Torkelson, S., Shrader, W.D., Kolesnikov, A., Rai, R., Liu, L., Hu, H., Leahy, E.M., Green, M.J., Sprengeler, P.A., Katz, B.A., Yu, C., Janc, J.W., Elrod, K.C., Marzec, U.M., Hanson, S.R.

(2006) Bioorg Med Chem Lett 16: 2037-2041

PubMed: 16412633 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2005.12.059
Primary Citation Related Structures:
2B7D

PubMed Abstract:
Highly selective and potent factor VIIa-tissue factor (fVIIa.TF) complex inhibitors were generated through structure-based design. The pharmacokinetic properties of an optimized analog (9) were characterized in several preclinical species, demonstrating pharmacokinetic characteristics suitable for once-a-day dosing in humans. Analog 9 inhibited platelet and fibrin deposition in a dose-dependent manner after intravenous administration in a baboon thrombosis model, and a pharmacodynamic concentration-response model was developed to describe the platelet deposition data. Results for heparin and enoxaparin (Lovenox) in the baboon model are also presented.

Organizational Affiliation

Celera Genomics, 180 Kimball Way, South San Francisco, CA 94080, USA. wendy.young@yahoo.com

Macromolecule Content

Total Structure Weight: 70.42 kDa
Atom Count: 4,233
Modeled Residue Count: 497
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

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| 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
C1B Query on C1B 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]	(2R)-2-[5-(5-CARBAMIMIDOYL-1H-BENZOIMIDAZOL-2-YL)-6,2'-DIHYDROXY-5'-UREIDOMETHYL-BIPHENYL-3-YL]-SUCCINIC ACID C₂₆ H₂₄ N₆ O₇ JCBJULMYEXYZRC-CQSZACIVSA-N		Interactions Focus chain D [auth H] Interactions & Density Focus chain D [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free: 0.289 (Depositor), 0.240 (DCC)
R-Value Work: 0.247 (Depositor), 0.240 (DCC)
R-Value Observed: 0.250 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.7	α = 90
b = 69.03	β = 89.49
c = 78.19	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-sight	model building
Accelrys	model building
X-PLOR	refinement
X-SIGHT	phasing
ACCELRYS	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-02-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-02-14
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: Refinement description
Version 1.4: 2023-08-23
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2024-10-16
Changes: Structure summary