2C93

thrombin inhibitors

Structural Biology Knowledgebase: 2C93 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.164

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2C93

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 35997.34

Macromolecule Entities
Molecule Chains Length Organism Details
THROMBIN, LIGHT CHAIN A 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: FRAGMENT ALPHA THROMBIN, RESIDUES 328-363
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
THROMBIN HEAVY CHAIN B 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: FRAGMENT ALPHA THROMBIN, RESIDUES 364-622
Gene Name(s): F2 Gene View
HIRUDIN VARIANT-2 I 12 Hirudo medicinalis Fragment: PEPTIDE FRAGMENT OF HIRUGEN, RESIDUES 61-72
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
C4M
Query on C4M

B N-[(2R,3S)-3-AMINO-2-HYDROXY-4-PHENYLBUTYL]- 4-METHOXY-2,3,6-TRIMETHYLBENZENESULFONAMIDE
INHIBITOR OF THROMBIN (Synonym)
C20 H28 N2 O4 S
HORGTFOBJRCVMO-ZWKOTPCHSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DMS
Query on DMS

B DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
C4M IC50: 12000 nM (100) BindingDB

IC50: 12000 nM  BindingMOAD
IC50: 12000 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
TYS
Query on TYS
I L-PEPTIDE LINKING C9 H11 N O6 S TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.164
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 70.66 α = 90.00
b = 71.56 β = 100.65
c = 71.96 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-12-09
  • Released Date: 2006-07-04
  • Deposition author(s): Howard, N., Abell, C., Blakemore, W., Carr, R., Chessari, G., Congreve, M., Howard, S., Jhoti, H., Murray, C.W., Seavers, L.C.A., van Montfort, R.L.M.

Revision History

  • 2015-04-15
    Type: Source and taxonomy | Details: SOURCE
  • 2013-08-07
    Type: Other | Details: REMARK 900
  • 2013-08-07
    Type: Biological assembly | Details: REMARK 350
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Version format compliance | Details: Compliance with PDBx exchange dictionary V4