1W0Y

tf7a_3771 complex

PDB DOI: https://doi.org/10.2210/pdb1W0Y/pdb

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

Deposited: 2004-05-27 Released: 2005-01-21
Deposition Author(s): Banner, D.W., D'Arcy, A., Groebke-Zbinden, K., Ackermann, J., Kirchhofer, D., Ji, Y.-H., Tschopp, T.B., Wallbaum, S., Weber, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.258
R-Value Work: 0.199

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

Design of Selective Phenylglycine Amide Tissue Factor/Factor Viia Inhibitors

Groebke-Zbinden, K., Banner, D.W., Ackermann, J., D'Arcy, A., Kirchhofer, D., Ji, Y.-H., Tschopp, T.B., Wallbaum, S., Weber, L.

(2005) Bioorg Med Chem Lett 15: 817

PubMed: 15664864 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2004.10.092
Primary Citation of Related Structures:
1W0Y, 1W2K

PubMed Abstract:
Proof of concept experiments have shown that tissue factor/factor VIIa inhibitors have antithrombotic activity without enhancing bleeding propensity. Starting from lead compounds generated by a biased combinatorial approach, phenylglycine amide tissue factor/factor VIIa inhibitors with low nanomolar affinity and good selectivity against other serine proteases of the coagulation cascade were designed, using the guidance of X-ray structural analysis and molecular modelling.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 69.48 kDa
Atom Count: 5,060
Modelled Residue Count: 581
Deposited Residue Count: 606
Unique protein chains: 3

Macromolecules

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(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
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
BLOOD COAGULATION FACTOR VIIA	B [auth L]	142	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
GTEx: ENSG00000057593
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08709
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain B [auth L]	Go to GlyGen: P08709-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TISSUE FACTOR	C [auth T]	210	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P13726 (Homo sapiens) Explore P13726 Go to UniProtKB: 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
771 Query on 771 Download Ideal Coordinates CCD File SDF format, chain D [auth H] MOL2 format, chain D [auth H]	D [auth H]	4-(4-BENZYLOXY-2-METHANESULFONYLAMINO-5-METHOXY-BENZYLAMINO)-BENZAMIDINE C₂₃ H₂₆ N₄ O₄ S CRFICMUDNBIMKL-UHFFFAOYSA-N		Interactions Focus chain D [auth H] Interactions & Density Focus chain D [auth H]
BGC Query on BGC Download Ideal Coordinates CCD File SDF format, chain P [auth L] MOL2 format, chain P [auth L]	P [auth L]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain P [auth L] Interactions & Density Focus chain P [auth L]
FUC Query on FUC Download Ideal Coordinates CCD File SDF format, chain G [auth L] MOL2 format, chain G [auth L]	G [auth L]	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain G [auth L] Interactions & Density Focus chain G [auth L]
CAC Query on CAC Download Ideal Coordinates CCD File SDF format, chain F [auth H] MOL2 format, chain F [auth H]	F [auth H]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain F [auth H] Interactions & Density Focus chain F [auth H]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth H] SDF format, chain H [auth L] SDF format, chain I [auth L] SDF format, chain J [auth L] SDF format, chain K [auth L] SDF format, chain L SDF format, chain M [auth L] SDF format, chain O [auth L] SDF format, chain N [auth L] MOL2 format, chain E [auth H] MOL2 format, chain H [auth L] MOL2 format, chain I [auth L] MOL2 format, chain J [auth L] MOL2 format, chain K [auth L] MOL2 format, chain L MOL2 format, chain M [auth L] MOL2 format, chain O [auth L] MOL2 format, chain N [auth L]	E [auth H] H [auth L] I [auth L] J [auth L] K [auth L] E [auth H], H [auth L], I [auth L], J [auth L], K [auth L], L, M [auth L], N [auth L], O [auth L]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Focus chain H [auth L] Focus chain I [auth L] Focus chain J [auth L] Focus chain K [auth L] Focus chain L Focus chain M [auth L] Focus chain N [auth L] Focus chain O [auth L] Interactions & Density Focus chain E [auth H] Focus chain H [auth L] Focus chain I [auth L] Focus chain J [auth L] Focus chain K [auth L] Focus chain L Focus chain M [auth L] Focus chain N [auth L] Focus chain O [auth L]

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

Binding Affinity Annotations
ID	Source	Binding Affinity
771	BindingDB: 1W0Y	Ki: 380 (nM) from 1 assay(s)
771	PDBBind: 1W0Y	Ki: 380 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.258
R-Value Work: 0.199
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.338	α = 90
b = 82.378	β = 90
c = 123.963	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
XDS	data reduction
XDS	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-01-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-01-21
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Other, Structure summary
Version 1.4: 2023-12-13
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary