2AEI | pdb_00002aei

Crystal structure of a ternary complex of factor VIIa/tissue factor and 2-[[6-[3-(aminoiminomethyl)phenoxy]-3,5-difluro-4-[(1-methyl-3-phenylpropyl)amino]-2-pyridinyl]oxy]-benzoic acid

PDB DOI: https://doi.org/10.2210/pdb2AEI/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Cricetulus griseus, Saccharomyces cerevisiae
Mutation(s): Yes

Deposited: 2005-07-22 Released: 2006-08-01
Deposition Author(s): Adler, M., Whitlow, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free:
0.297 (Depositor), 0.290 (DCC)
R-Value Work:
0.199 (Depositor), 0.210 (DCC)
R-Value Observed:
0.204 (Depositor)

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

The discovery of fluoropyridine-based inhibitors of the Factor VIIa/TF complex.

Kohrt, J.T., Filipski, K.J., Cody, W.L., Cai, C., Dudley, D.A., Van Huis, C.A., Willardsen, J.A., Rapundalo, S.T., Saiya-Cork, K., Leadley, R.J., Narasimhan, L., Zhang, E., Whitlow, M., Adler, M., McLean, K., Chou, Y.L., McKnight, C., Arnaiz, D.O., Shaw, K.J., Light, D.R., Edmunds, J.J.

(2005) Bioorg Med Chem Lett 15: 4752-4756

PubMed: 16125385 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2005.07.059
Primary Citation of Related Structures:
2AEI

PubMed Abstract:
The activated Factor VII/tissue factor complex (FVIIa/TF) plays a key role in the formation of blood clots. Inhibition of this complex may lead to new antithrombotic drugs. An X-ray crystal structure of a fluoropyridine-based FVIIa/TF inhibitor bound in the active site of the enzyme complex suggested that incorporation of substitution at the 5-position of the hydroxybenzoic acid side chain could lead to the formation of more potent inhibitors through interactions with the S1'/S2' pocket.

Organizational Affiliation

Pfizer Global Research and Development, Michigan Laboratories, 2800 Plymouth Road, Ann Arbor, MI 48105, USA. jeffrey.kohrt@pfizer.com

Macromolecule Content

Total Structure Weight: 70.4 kDa
Atom Count: 4,812
Modeled Residue Count: 591
Deposited Residue Count: 617
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII	A [auth L]	152	Homo sapiens	Mutation(s): 10 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	B [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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tissue factor	C [auth T]	211	Homo sapiens	Mutation(s): 0 Gene Names: F3
UniProt & NIH Common Fund Data Resources
Find proteins for P13726 (Homo sapiens) Explore P13726 Go to UniProtKB: P13726
PHAROS: P13726 GTEx: ENSG00000117525
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13726
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
03R Query on 03R Download Ideal Coordinates CCD File SDF format, chain M [auth H] MOL2 format, chain M [auth H] mmCIF format, chain M [auth H]	M [auth H]	2-({6-{3-[AMINO(IMINO)METHYL]PHENOXY}-3,5-DIFLUORO-4-[(1-METHYL-3-PHENYLPROPYL)AMINO]-2-PYRIDINYL}OXY)BENZOIC ACID C₂₉ H₂₆ F₂ N₄ O₄ BUZNVJZUYOBGFM-KRWDZBQOSA-N		Interactions Focus chain M [auth H] Interactions & Density Focus chain M [auth H]
CAC Query on CAC Download Ideal Coordinates CCD File SDF format, chain L [auth H] MOL2 format, chain L [auth H] mmCIF format, chain L [auth H]	L [auth H]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain L [auth H] Interactions & Density Focus chain L [auth H]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth L] SDF format, chain E [auth L] SDF format, chain F [auth L] SDF format, chain G [auth L] SDF format, chain H [auth L] SDF format, chain I [auth L] SDF format, chain J [auth L] SDF format, chain K [auth H] MOL2 format, chain D [auth L] MOL2 format, chain E [auth L] MOL2 format, chain F [auth L] MOL2 format, chain G [auth L] MOL2 format, chain H [auth L] MOL2 format, chain I [auth L] MOL2 format, chain J [auth L] MOL2 format, chain K [auth H] mmCIF format, chain D [auth L] mmCIF format, chain E [auth L] mmCIF format, chain F [auth L] mmCIF format, chain G [auth L] mmCIF format, chain H [auth L] mmCIF format, chain I [auth L] mmCIF format, chain J [auth L] mmCIF format, chain K [auth H]	D [auth L] E [auth L] F [auth L] G [auth L] H [auth L] D [auth L], E [auth L], F [auth L], G [auth L], H [auth L], I [auth L], J [auth L], K [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth L] Focus chain E [auth L] Focus chain F [auth L] Focus chain G [auth L] Focus chain H [auth L] Focus chain I [auth L] Focus chain J [auth L] Focus chain K [auth H] Interactions & Density Focus chain D [auth L] Focus chain E [auth L] Focus chain F [auth L] Focus chain G [auth L] Focus chain H [auth L] Focus chain I [auth L] Focus chain J [auth L] Focus chain K [auth H]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CGU Query on CGU	A [auth L]	L-PEPTIDE LINKING	C₆ H₉ N O₆		GLU

Binding Affinity Annotations
ID	Source	Binding Affinity
03R	BindingDB: 2AEI	IC50: 86 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free: 0.297 (Depositor), 0.290 (DCC)
R-Value Work: 0.199 (Depositor), 0.210 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.215	α = 90
b = 80.496	β = 90
c = 125.936	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MERLOT	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-08-01

Deposition Author(s):

Adler, M.

Whitlow, M.

Revision History (Full details and data files)

Version 1.0: 2006-08-01
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-11-15
Changes: Data collection