2BVX

Design and Discovery of Novel, Potent Thrombin Inhibitors with a Solubilizing Cationic P1-P2-Linker

PDB DOI: https://doi.org/10.2210/pdb2BVX/pdb

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

Deposited: 2005-07-04 Released: 2006-10-25
Deposition Author(s): Bulat, S., Bosio, S., Grabowski, E., Papadopoulos, M.A., Cerezo-Galvez, S., Rosenbaum, C., Matassa, V.G., Ott, I., Metz, G., Schamberger, J., Sekul, R., Feurer, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.306
R-Value Work: 0.219

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Design and Discovery of Novel, Potent Pyrazinone-Based Thrombin Inhibitors with a Solubilizing P1-P2-Linker

Bulat, S., Bosio, S., Papadopoulos, M.A., Cerezo-Galvez, S., Grabowski, E., Rosenbaum, C., Matassa, V.G., Ott, I., Metz, G., Schamberger, J., Sekul, R., Feurer, A.

(2006) Lett Drug Des Discov 3: 289-292

DOI: https://doi.org/10.2174/157018006777574203

Macromolecule Content

Total Structure Weight: 35.79 kDa
Atom Count: 2,431
Modelled Residue Count: 292
Deposited Residue Count: 306
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA THROMBIN	A [auth H]	259	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 P09945 (Hirudo medicinalis) Explore P09945 Go to UniProtKB: P09945
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09945
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA THROMBIN	C [auth L]	36	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5CB Query on 5CB 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]	N-(5-CHLORO-BENZO[B]THIOPHEN-3-YLMETHYL)-2-[6-CHLORO-OXO-3-(2-PYRIDIN-2-YL-ETHYLAMINO)-2H-PYRAZIN-1-YL]-ACETAMIDE C₂₂ H₂₃ Cl₂ N₅ O₂ S SOBGXPPOYFFGTK-UGKGYDQZSA-N		Interactions Focus chain D [auth H]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS Query on TYS	B [auth I]	L-PEPTIDE LINKING	C₉ H₁₁ N O₆ S		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
5CB	PDBBind: 2BVX	Ki: 2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.306
R-Value Work: 0.219
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.004	α = 90
b = 71.711	β = 100.75
c = 72.646	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-10-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-10-25
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: 2016-12-21
Changes: Database references, Source and taxonomy, Structure summary
Version 1.3: 2024-10-23
Changes: Data collection, Database references, Derived calculations, Structure summary