SMTL ID : 6rly.1

Human MMP12 (catalytic domain) in complex with AP316

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.114, H.118, H.124 Ligands: HAE.6, K8T.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.114, A:H.118, A:H.124, HAE.6 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.1 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.3, H2O.4 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 HAE: ACETOHYDROXAMIC ACID(Non-covalent)

HAE.6: 9 residues within 4Å: Chain A: I.76, A.78, H.79, H.114, E.115, H.118, H.124 Ligands: ZN.1, K8T.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.76 Hydrogen bonds: A:A.78

1 x K8T: 2-(3-oxidanyl-2-oxidanylidene-pyridin-1-yl)-~{N}-[2-(4-phenylphenyl)ethyl]ethanamide(Non-covalent)

K8T.7: 15 residues within 4Å: Chain A: G.75, I.76, L.77, T.111, H.114, E.115, A.130, V.131, F.133, P.134, T.135, Y.136, K.137 Ligands: ZN.1, HAE.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.111, A:H.114, A:V.131, A:Y.136 Hydrogen bonds: A:P.134 pi-Stacking: A:H.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsoukalidou, S. et al., Exploration of zinc-binding groups for the design of inhibitors for the oxytocinase subfamily of M1 aminopeptidases. Bioorg.Med.Chem. (2019)

Release Date

2020-03-11

Peptides

Macrophage metalloelastase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Macrophage metalloelastase

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