4H49

Crystal structure of the catalytic domain of MMP-12 in complex with a twin inhibitor.

Structural Biology Knowledgebase: 4H49 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.167

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4H49

Classification: hydrolase / hydrolase inhibitor

Total Structure Weight: 74040.31

Macromolecule Entities
Molecule Chains Length Organism Details
Macrophage metalloelastase A, B, C, D 159 Homo sapiens EC#: 3.4.24.65 IUBMB
Fragment: Human MMP12 catalytic domain
Mutation: F171D
Gene Name(s): MMP12 Gene View HME

Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
L29
Query on L29

B, C N,N'-bis(2-{(biphenyl-4-ylsulfonyl)[(2R)- 1-(hydroxyamino)-3-methyl-1-oxobutan-2-yl]amino}ethyl)benzene- 1,3-dicarboxamide (non-preferred name)
C46 H52 N6 O10 S2
JPMXJRBHCOULJI-NCRNUEESSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

A, B, C, D DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

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

A DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PGO
Query on PGO

A S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

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

A, B, C, D CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.167
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 47.44 α = 90.00
b = 106.49 β = 94.96
c = 65.88 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-09-17
  • Released Date: 2013-04-24
  • Deposition author(s): Antoni, C., Stura, E.A., Vera, L., Nuti, E., Carafa, L., Cassar-Lajeunesse, E., Dive, V., Rossello, A.

Revision History

  • 2015-08-12
    Type: Citation | Details: Citation update
  • 2014-10-08
    Type: Citation | Details: --
  • 2013-05-01
    Type: Citation | Details: --