2BVR | pdb_00002bvr

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 (Depositor) 
  • R-Value Work: 
    0.210 (Depositor) 

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


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ALPHA THROMBINA [auth H]252Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00734
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HIRUDIN VARIANT-2B [auth I]11Hirudo medicinalisMutation(s): 0 
UniProt
Find proteins for P09945 (Hirudo medicinalis)
Explore P09945 
Go to UniProtKB:  P09945
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09945
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ALPHA THROMBINC [auth L]36Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00734
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4CP
Query on 4CP
Download Ideal Coordinates CCD File 
D [auth H]2-[2-(4-CHLORO-PHENYLSULFANYL)-ACETYLAMINO]-3-(4-GUANIDINO-PHENYL)-PROPIONAMIDE
C18 H20 Cl N5 O2 S
IEEYGOJDTRVYGR-HNNXBMFYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TYS
Query on TYS		B [auth I]L-PEPTIDE LINKINGC9 H11 N O6 STYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free:  0.229 (Depositor) 
  • R-Value Work:  0.210 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.322α = 90
b = 71.702β = 100.28
c = 72.539γ = 90
Software Package:
Software NamePurpose
CNXrefinement

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

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
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