5PAB

Crystal Structure of Factor VIIa in complex with 1-[[3-[2-hydroxy-3-(1H-pyrrolo[3,2-c]pyridin-2-yl)phenyl]phenyl]methyl]-3-phenylurea

PDB DOI: https://doi.org/10.2210/pdb5PAB/pdb
Deposition Group: G_1002015 ExploreG_1002015

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

Deposited: 2016-11-10 Released: 2017-06-21
Deposition Author(s): Stihle, M., Mayweg, A., Roever, S., Rudolph, M.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.220
R-Value Work: 0.186
R-Value Observed: 0.188

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of a Factor VIIa complex

Mayweg, A., Roever, S., Rudolph, M.G.

To be published.

Macromolecule Content

Total Structure Weight: 36.25 kDa
Atom Count: 2,792
Modelled Residue Count: 303
Deposited Residue Count: 318
Unique protein chains: 2

Macromolecules

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(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

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII light chain	B [auth L]	64	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7XD Query on 7XD Download Ideal Coordinates CCD File SDF format, chain C [auth H] MOL2 format, chain C [auth H]	C [auth H]	1-[[3-[2-oxidanyl-3-(1~{H}-pyrrolo[3,2-c]pyridin-2-yl)phenyl]phenyl]methyl]-3-phenyl-urea C₂₇ H₂₂ N₄ O₂ MYWMHTLQFNYXPC-UHFFFAOYSA-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 K [auth H] SDF format, chain M [auth L] MOL2 format, chain K [auth H] MOL2 format, chain M [auth L]	K [auth H], M [auth L]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth H] Focus chain M [auth L] Interactions & Density Focus chain K [auth H] Focus chain M [auth L]
GOL Query on GOL 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 L MOL2 format, chain E [auth H] MOL2 format, chain F [auth H] MOL2 format, chain G [auth H] MOL2 format, chain L	E [auth H], F [auth H], G [auth H], L	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth H] Focus chain L Interactions & Density Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth H] Focus chain L
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain H MOL2 format, chain H	H	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H Interactions & Density Focus chain H
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth H] SDF format, chain I [auth H] SDF format, chain J [auth H] MOL2 format, chain D [auth H] MOL2 format, chain I [auth H] MOL2 format, chain J [auth H]	D [auth H], I [auth H], J [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth H] Focus chain I [auth H] Focus chain J [auth H] Interactions & Density Focus chain D [auth H] Focus chain I [auth H] Focus chain J [auth H]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MHO Query on MHO	A [auth H]	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S		MET

Binding Affinity Annotations
ID	Source	Binding Affinity
7XD	BindingDB: 5PAB	Ki: 61.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.220
R-Value Work: 0.186
R-Value Observed: 0.188
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.217	α = 90
b = 95.217	β = 90
c = 116.197	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-06-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-06-21
Type: Initial release
Version 1.1: 2018-02-21
Changes: Structure summary
Version 1.2: 2021-11-17
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2024-04-03
Changes: Data collection, Refinement description

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5PAB

Crystal Structure of Factor VIIa in complex with 1-[[3-[2-hydroxy-3-(1H-pyrrolo[3,2-c]pyridin-2-yl)phenyl]phenyl]methyl]-3-phenylurea

Crystal Structure of a Factor VIIa complex

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2