4ZXY | pdb_00004zxy

FACTOR VIIA IN COMPLEX WITH THE INHIBITOR (2R)-2-[(1-aminoisoquinolin-6-yl)amino]-4,11-diazatricyclo[14.2.2.1~6,10~]henicosa-1(18),6(21),7,9,16,19-hexaene-3,12-dione

PDB DOI: https://doi.org/10.2210/pdb4ZXY/pdb

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

Deposited: 2015-05-20 Released: 2015-07-22
Deposition Author(s): Wei, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free:
0.211 (Depositor), 0.215 (DCC)
R-Value Work:
0.190 (Depositor), 0.190 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure-Based Design of Macrocyclic Coagulation Factor VIIa Inhibitors.

Priestley, E.S., Cheney, D.L., DeLucca, I., Wei, A., Luettgen, J.M., Rendina, A.R., Wong, P.C., Wexler, R.R.

(2015) J Med Chem 58: 6225-6236

PubMed: 26151189 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.5b00788
Primary Citation Related Structures:
4ZXX, 4ZXY

PubMed Abstract:
On the basis of a crystal structure of a phenylpyrrolidine lead and subsequent molecular modeling results, we designed and synthesized a novel series of macrocyclic FVIIa inhibitors. The optimal 16-membered macrocycle was 60-fold more potent than an acyclic analog. Further potency optimization by incorporation of P1' alkyl sulfone and P2 methyl groups provided a macrocycle with TF/FVIIa Ki = 1.6 nM, excellent selectivity against a panel of seven serine proteases, and FVII-deficient prothrombin time EC2x = 1.2 μM. Discovery of this potent, selective macrocyclic scaffold opens new possibilities for the development of orally bioavailable FVIIa inhibitors.

Macromolecule Content

Total Structure Weight: 35.02 kDa
Atom Count: 2,610
Modeled Residue Count: 305
Deposited Residue Count: 309
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation 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% 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 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% 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
4T1 Query on 4T1 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]	(2R)-2-[(1-aminoisoquinolin-6-yl)amino]-4,11-diazatricyclo[14.2.2.1~6,10~]henicosa-1(18),6(21),7,9,16,19-hexaene-3,12-dione C₂₈ H₂₇ N₅ O₂ LXFPTSIBSQOGTO-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 E [auth H] SDF format, chain F [auth H] SDF format, chain G [auth H] MOL2 format, chain E [auth H] MOL2 format, chain F [auth H] MOL2 format, chain G [auth H] mmCIF format, chain E [auth H] mmCIF format, chain F [auth H] mmCIF format, chain G [auth H]	E [auth H], F [auth H], G [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth H] Interactions & Density Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth H]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H MOL2 format, chain H mmCIF format, chain H	H	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H Interactions & Density Focus chain 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]

Binding Affinity Annotations
ID	Source	Binding Affinity
4T1	BindingDB: 4ZXY	Ki: 400 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free: 0.211 (Depositor), 0.215 (DCC)
R-Value Work: 0.190 (Depositor), 0.190 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.4	α = 90
b = 94.4	β = 90
c = 107.85	γ = 90

Software Package:

Software Name	Purpose
BUSTER	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: 2015-07-22

Deposition Author(s):

Wei, A.

Revision History (Full details and data files)

Version 1.0: 2015-07-22
Type: Initial release
Version 1.1: 2015-08-26
Changes: Database references
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-20
Changes: Structure summary