2BVR

Human thrombin complexed with fragment-based small molecules occupying the S1 pocket

PDB DOI: https://doi.org/10.2210/pdb2BVR/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): Neumann, T., Junker, H.-D., Keil, O., Burkert, K., Ottleben, H., Gamer, J., Sekul, R., Deppe, H., Feurer, A., Tomandl, D., Metz, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.229
R-Value Work: 0.210

wwPDB Validation 3D Report Full Report

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

Literature

Discovery of Thrombin Inhibitor Fragments from Chemical Microarray Screening

Neumann, T., Junker, H.-D., Keil, O., Burkert, K., Ottleben, H., Gamer, J., Sekul, R., Deppe, H., Feurer, A., Tomandl, D., Metz, G.

(2005) Lett Drug Des Discov 2: 590-594

DOI: https://doi.org/10.2174/157018005774717343

Macromolecule Content

Total Structure Weight: 34.93 kDa
Atom Count: 2,814
Modelled Residue Count: 290
Deposited Residue Count: 299
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]	252	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
4CP Query on 4CP 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]	2-[2-(4-CHLORO-PHENYLSULFANYL)-ACETYLAMINO]-3-(4-GUANIDINO-PHENYL)-PROPIONAMIDE C₁₈ H₂₀ Cl N₅ O₂ S IEEYGOJDTRVYGR-HNNXBMFYSA-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
4CP	PDBBind: 2BVR	Ki: 2.00e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.229
R-Value Work: 0.210
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.322	α = 90
b = 71.702	β = 100.28
c = 72.539	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: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary