SMTL ID : 7xjo.1 (1 other biounit)

Crystal structure of human MMP-2 catalytic domain in complex with inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x RYH- KFB- GLU- ASP- DAB- LEU- EME- EOE- NH2: RYH-KFB-GLU-ASP-DAB-LEU-EME-EOE-NH2(Non-covalent)

RYH-KFB-GLU-ASP-DAB-LEU-EME-EOE-NH2.1: 29 residues within 4Å: Chain A: F.5, P.6, R.7, Y.74, G.81, L.82, L.83, A.84, H.85, A.86, F.87, A.88, V.93, G.94, L.117, V.118, H.121, H.125, E.130, H.131, A.137, L.138, A.140, P.141, I.142, Y.143, T.144 Ligands: ZN.2, B3P.7 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:F.5, A:Y.74, A:Y.74, A:L.82, A:L.83, A:L.83, A:F.87, A:F.87, A:V.93, A:V.118, A:L.138, A:Y.143, A:Y.143 Hydrogen bonds: A:L.83, A:A.84, A:A.86, A:A.86, A:A.88, A:E.130, A:I.142, A:T.144 Water bridges: A:R.7, A:R.7, A:T.91, A:H.131, A:H.131, A:H.131, A:P.141, A:P.141 Salt bridges: A:R.7, A:H.121, A:H.125, A:H.131

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.121, H.125, H.131 Ligands: RYH-KFB-GLU-ASP-DAB-LEU-EME-EOE-NH2.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.121, A:H.125, A:H.131, H2O.3 ZN.3: 4 residues within 4Å: Chain A: H.70, D.72, H.85, H.98 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.70, A:D.72, A:H.85, A:H.98

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 7 residues within 4Å: Chain A: D.77, G.78, K.79, D.80, L.82, D.100, E.103 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.77, A:G.78, A:D.80, A:L.82, A:D.100, A:E.103 CA.5: 5 residues within 4Å: Chain A: D.60, G.92, V.93, G.94, D.96 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.60, A:G.92, A:G.94, A:D.96, H2O.1, H2O.2 CA.6: 4 residues within 4Å: Chain A: T.24, D.26, D.101, E.103 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.26, A:D.101, A:E.103, H2O.2, H2O.5 CA.8: 3 residues within 4Å: Chain A: R.67, E.69 Ligands: CL.9 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:R.67, A:E.69

1 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.7: 5 residues within 4Å: Chain A: D.72, G.73, Y.74, P.75 Ligands: RYH-KFB-GLU-ASP-DAB-LEU-EME-EOE-NH2.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.74 Hydrogen bonds: A:D.72, A:Y.74, A:Y.74

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 4 residues within 4Å: Chain A: G.66, R.67, H.70 Ligands: CA.8 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takeuchi, T. et al., Discovery of Aryloxyphenyl-Heptapeptide Hybrids as Potent and Selective Matrix Metalloproteinase-2 Inhibitors for the Treatment of Idiopathic Pulmonary Fibrosis. J.Med.Chem. (2022)

Release Date

2022-06-29

Peptides

Matrix metalloproteinase-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Matrix metalloproteinase-2

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