3KEC

Crystal Structure of Human MMP-13 complexed with a phenyl-2H-tetrazole compound

Structural Biology Knowledgebase: 3KEC SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.204
  • R-Value Work: 0.169

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3KEC

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 39291.40

Macromolecule Entities
Molecule Chains Length Organism Details
Collagenase 3 A, B 167 Homo sapiens EC#: 3.4.24 IUBMB
Fragment: catalytic domain, UNP residues 104-270
Gene Name(s): MMP13 Gene View

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
3KE
Query on 3KE

A, B 4-{[({3-[2-(4-methoxybenzyl)-2H-tetrazol- 5-yl]phenyl}carbonyl)amino]methyl}benzoic acid
4-((3-(2-(4-methoxybenzyl)-2H-tetrazol-5- yl)benzamido)methyl)benzoic acid (Synonym)
C24 H21 N5 O4
VUTBCSIBPMXNCZ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HAE
Query on HAE

A, B ACETOHYDROXAMIC ACID
C2 H5 N O2
RRUDCFGSUDOHDG-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
3KE IC50: 58 - 130 nM (100) BindingDB

IC50: 130 nM  BindingMOAD
IC50: 58 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.204
  • R-Value Work: 0.169
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 133.21 α = 90.00
b = 72.35 β = 90.00
c = 36.36 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-10-25
  • Released Date: 2010-11-10
  • Deposition author(s): Shieh, H.-S., Pavlovsky, A.G., Collins, B., Schnute, M.E.

Revision History

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