2BVS

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.202 

wwPDB Validation   3D Report Full Report


This is version 2.0 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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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ALPHA THROMBINA [auth H]259Homo 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  
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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)
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Go to UniProtKB:  P09945
Entity Groups  
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UniProt GroupP09945
Sequence Annotations
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  • Reference Sequence
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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
2CE
Query on 2CE

Download Ideal Coordinates CCD File 
D [auth H]N-[2-(2-CARBAMOYLMETHOXY-ETHOXY)-ETHYL]-2-[2-(4-CHLORO-PHENYLSULFANYL)-ACETYLAMINO]-3-(4-GUANIDINO-PHENYL)-PROPIONAMIDE
C24 H31 Cl N6 O5 S
SUVIJSGBAJVXMV-FQEVSTJZSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TYS
Query on TYS
B [auth I]L-PEPTIDE LINKINGC9 H11 N O6 STYR
Binding Affinity Annotations 
IDSourceBinding Affinity
2CE PDBBind:  2BVS Ki: 8.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.202 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.004α = 90
b = 71.711β = 100.75
c = 72.646γ = 90
Software Package:
Software NamePurpose
CNXrefinement

Structure Validation

View Full Validation Report



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: Atomic model, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
  • Version 2.0: 2024-10-09
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary