2BVR

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


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 1.2 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.Discovery 2: 590


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALPHA THROMBIN
H
252Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HIRUDIN VARIANT-2
I
11Hirudo medicinalisMutation(s): 0 
Find proteins for P09945 (Hirudo medicinalis)
Go to UniProtKB:  P09945
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ALPHA THROMBIN
L
36Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4CP
Query on 4CP

Download SDF File 
Download CCD File 
H
2-[2-(4-CHLORO-PHENYLSULFANYL)-ACETYLAMINO]-3-(4-GUANIDINO-PHENYL)-PROPIONAMIDE
C18 H20 Cl N5 O2 S
IEEYGOJDTRVYGR-HNNXBMFYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
I
L-PEPTIDE LINKINGC9 H11 N O6 STYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4CPKi: 200000 nM PDBBIND
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 = 70.322α = 90.00
b = 71.702β = 100.28
c = 72.539γ = 90.00
Software Package:
Software NamePurpose
CNXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2016-12-21
    Type: Database references, Source and taxonomy, Structure summary