1K21

HUMAN THROMBIN-INHIBITOR COMPLEX

Structural Biology Knowledgebase: 1K21 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.216

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1K21

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 36320.48

Macromolecule Entities
Molecule Chains Length Organism Details
Prothrombin L 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: THROMBIN LIGHT CHAIN, Residues 323-363
Gene Name(s): F2 Gene View
Prothrombin H 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: THROMBIN HEAVY CHAIN, Residues 364-622
Gene Name(s): F2 Gene View
Hirudin variant-2 I 12 Hirudo medicinalis Fragment: Residues 60-71
Gene Name(s):

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

H {[(1R)-2-((2S)-2-{[(3-{[AMINO(IMINO)METHYL]AMINO}PROPYL)AMINO]CARBONYL}PIPERIDINYL)- 1-(CYCLOHEXYLMETHYL)-2-OXOETHYL]AMINO}ACETIC ACID
INOGATRAN (ASTRA-ZENECA) (Synonym)
C21 H38 N6 O4
CDPROXZBMHOBTQ-SJORKVTESA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

H N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

H SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
IGN IC50: 17 - 22400 nM (100) BindingDB
Ki: 3 - 15 nM (100) BindingDB

Ki: 4.2 nM  BindingMOAD
Ki: 4.2 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: 1.86 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.216
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 69.62 α = 90.00
b = 71.55 β = 100.12
c = 71.82 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-09-26
  • Released Date: 2002-05-08
  • Deposition author(s): Stubbs, M.T., Musil, D.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 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