SMTL ID : 6ela.1 (3 other biounits)

Crystal structure of MMP12 in complex with inhibitor BE4.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.114, H.118, H.124 Ligands: B9Z.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.114, A:H.118, A:H.124 ZN.2: 4 residues within 4Å: Chain A: H.64, D.66, H.79, H.92 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.64, A:D.66, A:H.79, A:H.92

3 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.54, G.86, I.87, G.88, D.90 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.54, A:G.86, A:G.88, A:D.90, H2O.1, H2O.3 CA.4: 3 residues within 4Å: Chain A: D.20, E.95, E.97 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.20, A:E.95, A:E.95, H2O.6, H2O.6 CA.5: 6 residues within 4Å: Chain A: D.71, G.72, G.74, I.76, D.94, E.97 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.71, A:G.72, A:G.74, A:I.76, A:D.94, A:E.97

1 x B9Z: (2~{S})-2-[2-[4-(4-methoxyphenyl)phenyl]sulfanylphenyl]pentanedioic acid(Non-covalent)

B9Z.6: 20 residues within 4Å: Chain A: G.75, I.76, L.77, A.78, L.110, T.111, H.114, E.115, H.118, H.124, A.130, V.131, F.133, P.134, T.135, Y.136, A.137, V.139 Ligands: ZN.1, DIO.7 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.76, A:T.111, A:H.114, A:Y.136, A:Y.136 Hydrogen bonds: A:A.78 Water bridges: A:A.137 Salt bridges: A:H.114, A:H.118, A:H.124 pi-Stacking: A:H.114

1 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.7: 5 residues within 4Å: Chain A: H.68, H.79, A.80, F.81 Ligands: B9Z.6 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nuti, E. et al., Development of Thioaryl-Based Matrix Metalloproteinase-12 Inhibitors with Alternative Zinc-Binding Groups: Synthesis, Potentiometric, NMR, and Crystallographic Studies. J. Med. Chem. (2018)

Release Date

2018-05-16

Peptides

Macrophage metalloelastase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Macrophage metalloelastase

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