4L19

Matrix metalloproteinase-13 complexed with selective inhibitor compound Q1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.199
  • R-Value Work: 0.134

Literature

Macromolecules
Sequence Display for 4L19

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 40281.63

Macromolecule Entities
Molecule Chains Length Organism Details
Collagenase 3 A, B 171 Homo sapiens EC#: 3.4.24 IUBMB
Fragment: Catalytic domain (UNP residues 104-274)
Gene Name(s): MMP13 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
1UA
Query on 1UA

A, B 2-[(4-methylbenzyl)sulfanyl]-3,5,6,7-tetrahydro- 4H-cyclopenta[d]pyrimidin-4-one
C15 H16 N2 O S
SEZPRMPVJMVCBV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

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

A, B FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
1UA IC50: 400 - 2400 nM (100) BindingDB
Ki: 824 nM (100) BindingDB

Ki: 800 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.199
  • R-Value Work: 0.134
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 135.32 α = 90.00
b = 36.03 β = 130.23
c = 95.81 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-06-02
  • Released Date: 2014-12-10
  • Deposition author(s): Minond, D., Spicer, T.P., Jiang, J., Taylor, A.B., Hart, P.J., Roush, W.R., Fields, G.B., Hodder, P.S.

Revision History

No revisions since initial release