1C1U

RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE PROTEASES

Structural Biology Knowledgebase: 1C1U SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.206

Literature

Macromolecules
Sequence Display for 1C1U

Classification: BLOOD CLOTTING / HYDROLASE INHIBITOR

Total Structure Weight: 35747.23

Macromolecule Entities
Molecule Chains Length Organism Details
ALPHA THROMBIN L 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: LIGHT CHAIN
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ALPHA THROMBIN H 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: HEAVY CHAIN
Details: COMPLEXED WITH (5-AMIDINO-2-BENZIMIDAZOLYL)(2-BENZIMIDAZOLYL)METHANE
Gene Name(s): F2 Gene View
ACETYL HIRUDIN I 11 Hirudo medicinalis Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

H (5-AMIDINO-2-BENZIMIDAZOLYL)(2-BENZIMIDAZOLYL)METHANE
HEMI-BABIM (Synonym)
C16 H14 N6
KKJYVDXDZURHMA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

H ZINC ION
Zn
PTFCDOFLOPIGGS-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 %)
BAI Ki: 1 - 2310 nM (100) BindingDB

N/A in BindingMoad
Ki: 5.6 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: 0.235
  • R-Value Work: 0.206
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 71.68 α = 90.00
b = 72.12 β = 101.62
c = 73.11 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-07-21
  • Released Date: 2000-07-26
  • Deposition author(s): Katz, B.A., Luong, C.

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: 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: Atom occupancy | Details: Restore author's atom occupancy
  • 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