5U6J

Factor VIIa in complex with the inhibitor 3-{[(2R)-17-ethyl-4-methyl-3,12-dioxo-7-[(propan-2-yl)sulfonyl]-13-oxa-4,11-diazatricyclo[14.2.2.1~6,10~]henicosa-1(18),6(21),7,9,16,19-hexaen-2-yl]amino}benzamide

PDB DOI: https://doi.org/10.2210/pdb5U6J/pdb

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

Deposited: 2016-12-08 Released: 2017-05-10
Deposition Author(s): Wei, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.220
R-Value Work: 0.185
R-Value Observed: 0.189

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Neutral macrocyclic factor VIIa inhibitors.

Wurtz, N.R., Parkhurst, B.L., DeLucca, I., Glunz, P.W., Jiang, W., Zhang, X., Cheney, D.L., Bozarth, J.M., Rendina, A.R., Wei, A., Harper, T., Luettgen, J.M., Wu, Y., Wong, P.C., Seiffert, D.A., Wexler, R.R., Priestley, E.S.

(2017) Bioorg Med Chem Lett 27: 2650-2654

PubMed: 28460818 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2017.04.008
Primary Citation of Related Structures:
5U6J

PubMed Abstract:
Factor VIIa (FVIIa) inhibitors have shown strong antithrombotic efficacy in preclinical thrombosis models with limited bleeding liabilities. Discovery of potent, orally active FVIIa inhibitors has been largely unsuccessful due to the requirement of a basic P1 group to interact with Asp189 in the S1 binding pocket, limiting their membrane permeability. We have combined recently reported neutral P1 binding substituents with a highly optimized macrocyclic chemotype to produce FVIIa inhibitors with low nanomolar potency and enhanced permeability.

Organizational Affiliation

Bristol-Myers Squibb Research and Development, Princeton, NJ 08534, United States. Electronic address: nicholas.wurtz@bms.com.

Macromolecule Content

Total Structure Weight: 35.34 kDa
Atom Count: 2,673
Modelled Residue Count: 306
Deposited Residue Count: 309
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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% 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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII Light Chain	B [auth L]	55	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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
82J Query on 82J Download Ideal Coordinates CCD File SDF format, chain C [auth H] MOL2 format, chain C [auth H]	C [auth H]	3-{[(2R)-17-ethyl-4-methyl-3,12-dioxo-7-[(propan-2-yl)sulfonyl]-13-oxa-4,11-diazatricyclo[14.2.2.1~6,10~]henicosa-1(18),6(21),7,9,16,19-hexaen-2-yl]amino}benzamide C₃₁ H₃₆ N₄ O₆ S KZSYSYPLRUUKEU-MUUNZHRXSA-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 E [auth H] SDF format, chain F [auth H] SDF format, chain G [auth H] SDF format, chain H MOL2 format, chain E [auth H] MOL2 format, chain F [auth H] MOL2 format, chain G [auth H] MOL2 format, chain 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 I [auth H] SDF format, chain J [auth H] MOL2 format, chain I [auth H] MOL2 format, chain J [auth H]	I [auth H], J [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth H] Focus chain J [auth H] Interactions & Density Focus chain I [auth H] Focus chain J [auth H]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth H] MOL2 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]

Binding Affinity Annotations
ID	Source	Binding Affinity
82J	Binding MOAD: 5U6J	Ki: 23 (nM) from 1 assay(s)
82J	BindingDB: 5U6J	Ki: min: 23, max: 610 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.220
R-Value Work: 0.185
R-Value Observed: 0.189
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.43	α = 90
b = 95.43	β = 90
c = 117.67	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
AMoRE	phasing
DENZO	data reduction
SCALEPACK	data scaling
HKL-2000	data reduction
HKL-2000	data scaling
HKL-2000	data reduction
HKL-2000	data scaling
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-05-10

Deposition Author(s):

Wei, A.

Revision History (Full details and data files)

Version 1.0: 2017-05-10
Type: Initial release
Version 1.1: 2017-05-17
Changes: Database references
Version 1.2: 2017-06-07
Changes: Database references
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description