1WSS | pdb_00001wss

Human Factor Viia-Tissue Factor in Complex with peptide-mimetic inhibitor that has two charged groups in P2 and P4

PDB DOI: https://doi.org/10.2210/pdb1WSS/pdb

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

Deposited: 2004-11-10 Released: 2005-11-10
Deposition Author(s): Kadono, S., Sakamoto, A., Kikuchi, Y., Oh-Eda, M., Yabuta, N., Koga, T., Hattori, K., Shiraishi, T., Haramura, M., Kodama, H., Ono, Y., Esaki, T., Sato, H., Watanabe, Y., Itoh, S., Ohta, M., Kozono, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.282 (Depositor), 0.244 (DCC)
R-Value Work:
0.218 (Depositor), 0.195 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Structure of human factor VIIa/tissue factor in complex with a peptide-mimetic inhibitor: high selectivity against thrombin by introducing two charged groups in P2 and P4.

Kadono, S., Sakamoto, A., Kikuchi, Y., Oh-Eda, M., Yabuta, N., Koga, T., Hattori, K., Shiraishi, T., Haramura, M., Kodama, H., Ono, Y., Esaki, T., Sato, H., Watanabe, Y., Itoh, S., Ohta, M., Kozono, T.

(2005) Acta Crystallogr Sect F Struct Biol Cryst Commun 61: 169-173

PubMed: 16510984 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1744309105000047
Primary Citation Related Structures:
1WSS

PubMed Abstract:
The crystal structure of human factor VIIa/soluble tissue factor (FVIIa/sTF) in complex with a highly selective peptide-mimetic FVIIa inhibitor which shows 1670-fold selectivity against thrombin inhibition has been solved at 2.6 A resolution. The inhibitor is bound to FVIIa/sTF at the S1, S2 and S3 sites and at the additional S1 subsite. Two charged groups, the amidino group in P2 and the carboxylate group in P4, form ionic interactions with Asp60 and Lys192 of FVIIa, respectively. Structural comparisons between factor VIIa and thrombin show that thrombin has oppositely charged residues, Lys60F and Glu192, in the S2 site and the S1 subsites, respectively. These data suggest that the utilization of the differences of charge distribution in the S2 site and the S1 subsites between FVIIa and thrombin is critical for achieving high selectivity against thrombin inhibition. These results will provide valuable information for the structure-based drug design of specific inhibitors for FVIIa/TF.

Organizational Affiliation

Fuji Gotemba Research Laboratories, Chugai Pharmaceutical Co. Ltd, 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan. kadonosuj@chugai-pharm.co.jp

Macromolecule Content

Total Structure Weight: 71.58 kDa
Atom Count: 5,055
Modeled Residue Count: 587
Deposited Residue Count: 624
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII	A [auth L]	152	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08709
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A [auth L]	Go to GlyGen: P08709-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII	B [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% 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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tissue factor	C [auth T]	218	Homo sapiens	Mutation(s): 0
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13726
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3CB Query on 3CB Download:Ideal Coordinates CCD File SDF format, chain O [auth H] MOL2 format, chain O [auth H] mmCIF format, chain O [auth H]	O [auth H]	N-[(3-CARBOXYBENZYL)SULFONYL]ISOLEUCYL-N~1~-{4-[AMINO(IMINO)METHYL]BENZYL}-5-IMINOORNITHINAMIDE C₂₇ H₃₇ N₇ O₆ S UBGNMISWPGURDN-XORNHQRDSA-N		Interactions Focus chain O [auth H] Interactions & Density Focus chain O [auth H]
BGC Query on BGC Download:Ideal Coordinates CCD File SDF format, chain D [auth L] MOL2 format, chain D [auth L] mmCIF format, chain D [auth L]	D [auth L]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain D [auth L] Interactions & Density Focus chain D [auth L]
FUC Query on FUC Download:Ideal Coordinates CCD File SDF format, chain E [auth L] MOL2 format, chain E [auth L] mmCIF format, chain E [auth L]	E [auth L]	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain E [auth L] Interactions & Density Focus chain E [auth L]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain H [auth L] SDF format, chain I [auth L] SDF format, chain J [auth L] SDF format, chain L SDF format, chain M [auth L] SDF format, chain N [auth H] SDF format, chain K [auth L] SDF format, chain G [auth L] SDF format, chain F [auth L] MOL2 format, chain H [auth L] MOL2 format, chain I [auth L] MOL2 format, chain J [auth L] MOL2 format, chain L MOL2 format, chain M [auth L] MOL2 format, chain N [auth H] MOL2 format, chain K [auth L] MOL2 format, chain G [auth L] MOL2 format, chain F [auth L] mmCIF format, chain H [auth L] mmCIF format, chain I [auth L] mmCIF format, chain J [auth L] mmCIF format, chain L mmCIF format, chain M [auth L] mmCIF format, chain N [auth H] mmCIF format, chain K [auth L] mmCIF format, chain G [auth L] mmCIF format, chain F [auth L]	F [auth L] G [auth L] H [auth L] I [auth L] J [auth L] F [auth L], G [auth L], H [auth L], I [auth L], J [auth L], K [auth L], L, M [auth L], N [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions 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 L] Focus chain L Focus chain M [auth L] Focus chain N [auth H] Interactions & Density 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 L] Focus chain L Focus chain M [auth L] Focus chain N [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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.282 (Depositor), 0.244 (DCC)
R-Value Work: 0.218 (Depositor), 0.195 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.56	α = 90
b = 82.3	β = 90
c = 123.52	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2005-11-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-11-10
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2014-07-23
Changes: Structure summary
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Structure summary
Version 1.5: 2023-10-25
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary
Version 1.6: 2023-11-15
Changes: Data collection