1W7X

Factor7 - 413 complex

PDB DOI: https://doi.org/10.2210/pdb1W7X/pdb

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

Deposited: 2004-09-14 Released: 2005-10-25
Deposition Author(s): Ackermann, J., Alig, L., Banner, D.W., Boehm, H.-J., Groebke-Zbinden, K., Hilpert, K., Lave, T., Kuehne, H., Obst-Sander, U., Riederer, M.A., Stahl, M., Tschopp, T.B., Weber, L., Wessel, H.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.195 (Depositor), 0.195 (DCC)
R-Value Work:
0.169 (Depositor), 0.169 (DCC)
R-Value Observed:
0.170 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Selective and Orally Bioavailable Phenylglycine Tissue Factor/Factor Viia Inhibitors.

Zbinden, K.G., Obst-Sander, U., Hilpert, K., Kuhne, H., Banner, D.W., Bohm, H.J., Stahl, M., Ackermann, J., Alig, L., Weber, L., Wessel, H.P., Riederer, M.A., Tschopp, T.B., Lave, T.

(2005) Bioorg Med Chem Lett 15: 5344

PubMed: 16213138 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2005.04.079
Primary Citation of Related Structures:
1W7X, 1W8B

PubMed Abstract:
We describe the structure-based design and synthesis of highly potent, orally bioavailable tissue factor/factor VIIa inhibitors which interfere with the coagulation cascade by selective inhibition of the extrinsic pathway.

Organizational Affiliation

F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland. katrin.groebke_zbinden@roche.com

Macromolecule Content

Total Structure Weight: 35.28 kDa
Atom Count: 3,008
Modelled Residue Count: 302
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
BLOOD COAGULATION FACTOR VIIA	A [auth H]	254	Homo sapiens	Mutation(s): 0 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 LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BLOOD COAGULATION FACTOR VIIA	B [auth L]	55	Homo sapiens	Mutation(s): 0 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 LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
413 Query on 413 Download Ideal Coordinates CCD File SDF format, chain F [auth H] MOL2 format, chain F [auth H] mmCIF format, chain F [auth H]	F [auth H]	(S)-[(R)-2-(4-BENZYLOXY-3-METHOXY-PHENYL)-2-(4-CARBAMIMIDOYL-PHENYLAMINO)-ACETYLAMINO]-PHENYL-ACETIC ACID C₃₁ H₃₀ N₄ O₅ WGEGXJPYFSZDMU-IZLXSDGUSA-N		Interactions Focus chain F [auth H] Interactions & Density Focus chain F [auth H]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth H] SDF format, chain H SDF format, chain I [auth H] SDF format, chain J [auth L] MOL2 format, chain G [auth H] MOL2 format, chain H MOL2 format, chain I [auth H] MOL2 format, chain J [auth L] mmCIF format, chain G [auth H] mmCIF format, chain H mmCIF format, chain I [auth H] mmCIF format, chain J [auth L]	G [auth H], H, I [auth H], J [auth L]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth H] Focus chain H Focus chain I [auth H] Focus chain J [auth L] Interactions & Density Focus chain G [auth H] Focus chain H Focus chain I [auth H] Focus chain J [auth L]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth H] Focus chain D [auth H] Interactions & Density Focus chain C [auth H] Focus chain D [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
413	BindingDB: 1W7X	Ki: 4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.195 (Depositor), 0.195 (DCC)
R-Value Work: 0.169 (Depositor), 0.169 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95	α = 90
b = 95	β = 90
c = 115.85	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-10-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-10-25
Type: Initial release
Version 1.1: 2011-06-02
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-06-28
Changes: Data collection
Version 1.4: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Other, Structure summary