SMTL ID : 8h78.1 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.121, H.125, H.131 Ligands: L2U.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.121, A:H.125, A:H.131 ZN.2: 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

3 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: D.77, G.78, 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.4: 6 residues within 4Å: Chain A: A.59, D.60, G.92, V.93, G.94, D.96 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.60, A:G.92, A:D.96 CA.5: 4 residues within 4Å: Chain A: T.24, D.26, D.101, E.103 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.26, A:D.101, A:D.101, A:E.103

1 x 2HP: DIHYDROGENPHOSPHATE ION(Non-covalent)

2HP.6: 4 residues within 4Å: Chain A: G.81, L.83, Y.143 Ligands: L2U.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.143

1 x L2U: (2~{R})-2-[[4-[(4-aminocarbonylphenyl)carbonylamino]phenyl]sulfonylamino]-5-[(2~{S},4~{S})-4-azanyl-2-[[(2~{S})-1-[[(2~{S})-1-[(5-azanyl-5-oxidanylidene-pentyl)amino]-5-oxidanyl-1,5-bis(oxidanylidene)pentan-2-yl]-methyl-amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamoyl]pyrrolidin-1-yl]-5-oxidanylidene-pentanoic acid(Non-covalent)

L2U.7: 30 residues within 4Å: Chain A: F.5, P.6, Y.74, G.81, L.82, L.83, A.84, H.85, A.86, F.87, A.88, G.90, T.91, 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, F.149 Ligands: ZN.1, 2HP.6 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:F.5, A:F.5, A:Y.74, A:Y.74, A:L.83, A:F.87, A:F.87, A:L.117, A:H.121, A:L.138, A:Y.143 Hydrogen bonds: A:L.83, A:A.84, A:A.84, A:A.86, A:A.86, A:A.88, A:T.91, A:G.94, A:E.130, A:A.140, A:T.144 Salt bridges: A:H.121, A:H.125, A:H.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takeuchi, T. et al., Discovery of TP0597850: A Selective, Chemically Stable, and Slow Tight-Binding Matrix Metalloproteinase-2 Inhibitor with a Phenylbenzamide-Pentapeptide Hybrid Scaffold. J.Med.Chem. (2023)

Release Date

2023-01-18

Peptides

Matrix metalloproteinase-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Matrix metalloproteinase-2

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