4YT6 | pdb_00004yt6

Factor VIIa in complex with the inhibitor 4-{[(R)-[5-ethoxy-2-fluoro-3-(propan-2-yloxy)phenyl](4-phenyl-1H-imidazol-2-yl)methyl]amino}benzenecarboximidamide

PDB DOI: https://doi.org/10.2210/pdb4YT6/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Cricetinae
Mutation(s): No

Deposited: 2015-03-17 Released: 2015-04-29
Deposition Author(s): Wei, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free:
0.202 (Depositor), 0.204 (DCC)
R-Value Work:
0.177 (Depositor), 0.175 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Design and synthesis of potent, selective phenylimidazole-based FVIIa inhibitors.

Glunz, P.W., Cheng, X., Cheney, D.L., Weigelt, C.A., Wei, A., Luettgen, J.M., Wong, P.C., Wexler, R.R., Priestley, E.S.

(2015) Bioorg Med Chem Lett 25: 2169-2173

PubMed: 25881820 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2015.03.062
Primary Citation Related Structures:
4YT6, 4YT7

PubMed Abstract:
Heterocyclic amide isosteres were incorporated into a phenylglycine-based tissue factor/factor VIIa (TF-FVIIa) inhibitor chemotype, providing potent inhibitors. An X-ray co-crystal structure of phenylimidazole 19 suggested that an imidazole nitrogen atom effectively mimics an amide carbonyl, while the phenyl ring forms key hydrophobic interactions with the S1' pocket. Exploration of phenylimidazole substitution led to the discovery of potent, selective and efficacious inhibitors of TF-FVIIa.

Organizational Affiliation

Bristol-Myers Squibb R&D, 311 Pennington-Rocky Hill Rd, Pennington, NJ 08534, United States. Electronic address: peter.glunz@bms.com.

Macromolecule Content

Total Structure Weight: 35.56 kDa
Atom Count: 2,771
Modeled Residue Count: 309
Deposited Residue Count: 311
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII (heavy chain)	A [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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII (light chain)	B [auth L]	57	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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4JY Query on 4JY Download:Ideal Coordinates CCD File SDF format, chain C [auth H] MOL2 format, chain C [auth H] mmCIF format, chain C [auth H]	C [auth H]	4-[[(R)-(5-ethoxy-2-fluoranyl-3-propan-2-yloxy-phenyl)-(4-phenyl-1H-imidazol-2-yl)methyl]amino]benzenecarboximidamide C₂₈ H₃₀ F N₅ O₂ FEJKACPKVXNBAK-AREMUKBSSA-N		Interactions Focus chain C [auth H] Interactions & Density Focus chain C [auth H]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth H] SDF format, chain H SDF format, chain F [auth H] SDF format, chain E [auth H] MOL2 format, chain G [auth H] MOL2 format, chain H MOL2 format, chain F [auth H] MOL2 format, chain E [auth H] mmCIF format, chain G [auth H] mmCIF format, chain H mmCIF format, chain F [auth H] mmCIF format, chain E [auth H]	E [auth H], F [auth H], G [auth H], H	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth H] Focus chain H Interactions & Density Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth H] Focus chain H
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth H] SDF format, chain K [auth H] SDF format, chain I [auth H] MOL2 format, chain J [auth H] MOL2 format, chain K [auth H] MOL2 format, chain I [auth H] mmCIF format, chain J [auth H] mmCIF format, chain K [auth H] mmCIF format, chain I [auth H]	I [auth H], J [auth H], K [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth H] Interactions & Density Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth H]
CA Query on CA 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]	CALCIUM ION Ca BHPQYMZQTOCNFJ-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: 2.07 Å
R-Value Free: 0.202 (Depositor), 0.204 (DCC)
R-Value Work: 0.177 (Depositor), 0.175 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.24	α = 90
b = 95.24	β = 90
c = 117.18	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-04-29

Deposition Author(s):

Wei, A.

Revision History (Full details and data files)

Version 1.0: 2015-04-29
Type: Initial release
Version 1.1: 2015-05-13
Changes: Database references
Version 2.0: 2023-09-27
Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy
Version 2.1: 2024-10-09
Changes: Structure summary