4JZD

Structure of factor VIIA in complex with the inhibitor 2-{2-[(4-carbamimidoylphenyl)carbamoyl]-6-methoxypyridin-3-yl}-5-{[(2S)-1-hydroxy-3,3-dimethylbutan-2-yl]carbamoyl}benzoic acid

PDB DOI: https://doi.org/10.2210/pdb4JZD/pdb

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

Deposited: 2013-04-02 Released: 2013-08-21
Deposition Author(s): Jacobson, B.L., Anumula, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.197
R-Value Work: 0.164
R-Value Observed: 0.166

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Discovery of nonbenzamidine factor VIIa inhibitors using a biaryl acid scaffold.

Bolton, S.A., Sutton, J.C., Anumula, R., Bisacchi, G.S., Jacobson, B., Slusarchyk, W.A., Treuner, U.D., Wu, S.C., Zhao, G., Pi, Z., Sheriff, S., Smirk, R.A., Bisaha, S., Cheney, D.L., Wei, A., Schumacher, W.A., Hartl, K.S., Liu, E., Zahler, R., Seiler, S.M.

(2013) Bioorg Med Chem Lett 23: 5239-5243

PubMed: 23927973 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2013.06.028
Primary Citation of Related Structures:
4JZD, 4JZE, 4JZF

PubMed Abstract:
In this Letter, we describe the synthesis of several nonamidine analogs of biaryl acid factor VIIa inhibitor 1 containing weakly basic or nonbasic P1 groups. 2-Aminoisoquinoline was found to be an excellent surrogate for the benzamidine group (compound 2) wherein potent inhibition of factor VIIa is maintained relative to most other related serine proteases. In an unanticipated result, the m-benzamide P1 (compounds 21a and 21b) proved to be a viable benzamidine replacement, albeit with a 20-40 fold loss in potency against factor VIIa.

Organizational Affiliation

Bristol-Myers Squibb Research & Development, Hopewell, NJ 08534-5400, USA. scott.bolton@bms.com

Macromolecule Content

Total Structure Weight: 35.91 kDa
Atom Count: 2,808
Modelled Residue Count: 309
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
Factor VIIa (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
Factor VIIa (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
1NJ Query on 1NJ Download Ideal Coordinates CCD File SDF format, chain C [auth H] SDF format, chain D [auth H] MOL2 format, chain C [auth H] MOL2 format, chain D [auth H] mmCIF format, chain C [auth H] mmCIF format, chain D [auth H]	C [auth H], D [auth H]	2-{2-[(4-carbamimidoylphenyl)carbamoyl]-6-methoxypyridin-3-yl}-5-{[(2S)-1-hydroxy-3,3-dimethylbutan-2-yl]carbamoyl}benzoic acid C₂₈ H₃₁ N₅ O₆ KPACBFJTZSMBKD-OAQYLSRUSA-N		Interactions Focus chain C [auth H] Focus chain D [auth H] Interactions & Density Focus chain C [auth H] Focus chain D [auth H]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth H] SDF format, chain G [auth H] SDF format, chain H SDF format, chain I [auth H] SDF format, chain J [auth H] SDF format, chain L MOL2 format, chain F [auth H] MOL2 format, chain G [auth H] MOL2 format, chain H MOL2 format, chain I [auth H] MOL2 format, chain J [auth H] MOL2 format, chain L mmCIF format, chain F [auth H] mmCIF format, chain G [auth H] mmCIF format, chain H mmCIF format, chain I [auth H] mmCIF format, chain J [auth H] mmCIF format, chain L	F [auth H] G [auth H] H I [auth H] J [auth H] F [auth H], G [auth H], H, I [auth H], J [auth H], L	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain I [auth H] Focus chain J [auth H] Focus chain L Interactions & Density Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain I [auth H] Focus chain J [auth H] Focus chain L
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth H] MOL2 format, chain K [auth H] mmCIF format, chain K [auth H]	K [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth H] Interactions & Density Focus chain K [auth H]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth H] MOL2 format, chain E [auth H] mmCIF format, chain E [auth H]	E [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Interactions & Density Focus chain E [auth H]

Binding Affinity Annotations
ID	Source	Binding Affinity
1NJ	BindingDB: 4JZD	Ki: 10 (nM) from 1 assay(s)
	BindingDB: 4JZD	IC50: 5 (nM) from 1 assay(s)
	PDBBind: 4JZD	IC50: 5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.197
R-Value Work: 0.164
R-Value Observed: 0.166
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.83	α = 90
b = 94.83	β = 90
c = 118.49	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-08-21

Deposition Author(s):

Jacobson, B.L.

Anumula, R.

Revision History (Full details and data files)

Version 1.0: 2013-08-21
Type: Initial release
Version 1.1: 2013-09-04
Changes: Database references
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-30
Changes: Structure summary