SMTL ID : 5uwn.4 (4 other biounits)

Matrix metalloproteinase-13 complexed with selective inhibitor compound 10d

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.120, E.121, H.124, H.130 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.120, A:H.124, A:H.130 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

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: D.77, G.78, S.80, L.82, D.100, E.103 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.77, A:G.78, A:S.80, A:L.82, A:D.100 CA.4: 5 residues within 4Å: Chain A: A.59, D.60, N.92, G.94, D.96 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.60, A:N.92, A:G.94, A:D.96

1 x 8O7: N-(2-aminoethyl)-4'-(((4-oxo-4,5,6,7-tetrahydro-3H-cyclopenta[d]pyrimidin-2-yl)thio)methyl)-[1,1'-biphenyl]-4-sulfonami de(Non-covalent)

8O7.5: 19 residues within 4Å: Chain A: L.82, L.83, A.84, L.116, V.117, H.120, E.121, G.135, A.136, L.137, F.139, P.140, I.141, Y.142, T.143, Y.144, T.145, F.150, P.153 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.83, A:L.83, A:V.117, A:H.120, A:Y.142, A:F.150, A:P.153 Hydrogen bonds: A:A.84, A:T.143, A:T.143, A:T.145 pi-Stacking: A:H.120

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 3 residues within 4Å: Chain A: K.13, M.14, N.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.14, A:N.15, A:N.15 SO4.7: 3 residues within 4Å: Chain A: T.28, H.29 Ligands: SO4.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.29 Salt bridges: A:H.29 SO4.8: 3 residues within 4Å: Chain A: T.28, S.30 Ligands: SO4.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.30, A:S.30 SO4.9: 3 residues within 4Å: Chain A: Y.18, K.37, R.53 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.18 Salt bridges: A:K.37, A:R.53 SO4.10: 4 residues within 4Å: Chain A: T.106, S.108, S.109, K.110 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.108, A:S.108, A:S.109, A:K.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Choi, J.Y. et al., Structure-Based Design and Synthesis of Potent and Selective Matrix Metalloproteinase 13 Inhibitors. J. Med. Chem. (2017)

Release Date

2017-07-12

Peptides

Collagenase 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Collagenase 3

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