1VZQ

Complex of thrombin with designed inhibitor 7165

PDB DOI: https://doi.org/10.2210/pdb1VZQ/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens, Hirudo medicinalis
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2004-05-24 Released: 2005-06-20
Deposition Author(s): Shaerer, K., Morgenthaler, M., Seiler, P., Diederich, F., Banner, D.W., Tschopp, T., Obst-Sander, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.209
R-Value Work: 0.181

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Enantiomerically Pure Thrombin Inhibitors for Exploring the Molecular-Recognition Features of the Oxyanion Hole

Schaerer, K., Morgenthaler, M., Seiler, P., Diederich, F., Banner, D.W., Tschopp, T., Obst-Sander, U.

(2004) Helv Chim Acta 87: 2517

Macromolecule Content

Total Structure Weight: 33.86 kDa
Atom Count: 2,739
Modelled Residue Count: 284
Deposited Residue Count: 288
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THROMBIN HEAVY	A [auth H]	250	Homo sapiens	Mutation(s): 0 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734 Go to UniProtKB: P00734
PHAROS: P00734 GTEx: ENSG00000180210
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00734
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIRUDIN VARIANT-2	B [auth I]	11	Hirudo medicinalis	Mutation(s): 0
UniProt
Find proteins for P28504 (Hirudo medicinalis) Explore P28504 Go to UniProtKB: P28504
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28504
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
THROMBIN LIGHT	C [auth L]	27	Homo sapiens	Mutation(s): 0 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734 Go to UniProtKB: P00734
PHAROS: P00734 GTEx: ENSG00000180210
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00734
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SHY Query on SHY Download Ideal Coordinates CCD File SDF format, chain D [auth H] MOL2 format, chain D [auth H] mmCIF format, chain D [auth H]	D [auth H]	4-[(3AS,4R,7R,8AS,8BR)-2-(1,3-BENZODIOXOL-5-YLMETHYL)-7-HYDROXY-1,3-DIOXODECAHYDROPYRROLO[3,4-A]PYRROLIZIN-4-YL]BENZENECARBOXIMIDAMIDE C₂₄ H₂₄ N₄ O₅ CETLUACQMGBMFH-ZALSBGIRSA-N		Interactions Focus chain D [auth H] Interactions & Density Focus chain D [auth H]
CA Query on CA 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]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth H] Interactions & Density Focus chain F [auth H]
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Interactions & Density Focus chain E [auth H]

Binding Affinity Annotations
ID	Source	Binding Affinity
SHY	PDBBind: 1VZQ	Ki: 36 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.209
R-Value Work: 0.181
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.9	α = 90
b = 71.4	β = 100.4
c = 72.4	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-06-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-06-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
Version 1.2: 2017-06-28
Changes: Data collection
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.4: 2024-10-23
Changes: Structure summary