1O5G

Dissecting and Designing Inhibitor Selectivity Determinants at the S1 site Using an Artificial Ala190 Protease (Ala190 uPA)

Structural Biology Knowledgebase: 1O5G SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.208

Literature

Macromolecules
Sequence Display for 1O5G

Classification: BLOOD CLOTTING HYDROLASE / INHIBITOR

Total Structure Weight: 35814.04

Macromolecule Entities
Molecule Chains Length Organism Details
Prothrombin L 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: LIGHT CHAIN, RESIDUES 328-363
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Prothrombin H 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: HEAVY CHAIN, RESIDUES 364-620
Gene Name(s): F2 Gene View
Hirudin IIIB' I 11 Hirudo medicinalis Mutation: Y63X
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CR9
Query on CR9

H 2-{5-[AMINO(IMINIO)METHYL]-6-FLUORO-1H-BENZIMIDAZOL- 2-YL}-6-[(2-METHYLCYCLOHEXYL)OXY]BENZENOLATE
CRA_11092 (Synonym)
C21 H23 F N4 O2
CMCDWLMEDRBWIR-GTNSWQLSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

H CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

H SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
CR9 Ki: 11000 nM (100) BindingDB

Ki: 11000 nM  BindingMOAD
Ki: 11000 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: 1.75 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.208
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 71.34 α = 90.00
b = 72.04 β = 100.83
c = 72.95 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-09-09
  • Released Date: 2004-09-21
  • Deposition author(s): Katz, B.A., Luong, C., Ho, J.D., Somoza, J.R., Gjerstad, E., Tang, J., Williams, S.R., Verner, E., Mackman, R.L., Young, W.B., Sprengeler, P.A., Chan, H., Mortara, K., Janc, J.W., McGrath, M.E.

Revision History

  • 2013-03-13
    Type: Other | Details: Remove PRD info on PRD molecule with WAIT status
  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 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 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