SMTL ID : 4l19.2 (2 other biounits)

Matrix metalloproteinase-13 complexed with selective inhibitor compound Q1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.69, D.71, H.84, H.97 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.69, A:D.71, A:H.84, A:H.97 ZN.2: 4 residues within 4Å: Chain A: H.119, H.123, H.129 Ligands: FMT.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.119, A:H.123, A:H.129

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.59, N.91, G.93, D.95 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.59, A:N.91, A:G.93, A:D.95, H2O.4, H2O.5 CA.4: 6 residues within 4Å: Chain A: D.76, G.77, S.79, L.81, D.99, E.102 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.76, A:G.77, A:S.79, A:L.81, A:D.99, A:E.102

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.5: 6 residues within 4Å: Chain A: A.83, H.119, E.120, H.123, H.129 Ligands: ZN.2 No protein-ligand interaction detected (PLIP) FMT.6: 2 residues within 4Å: Chain A: T.27, H.28 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.28 Water bridges: A:T.27, A:S.29 FMT.7: 1 residues within 4Å: Chain A: K.131 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.131 FMT.8: 3 residues within 4Å: Chain A: K.12, M.13, N.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.13, A:N.14, A:N.14

1 x 1UA: 2-[(4-methylbenzyl)sulfanyl]-3,5,6,7-tetrahydro-4H-cyclopenta[d]pyrimidin-4-one(Non-covalent)

1UA.9: 13 residues within 4Å: Chain A: L.115, V.116, H.119, G.134, L.136, F.138, P.139, I.140, Y.141, T.142, T.144, F.149, P.152 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:H.119, A:Y.141, A:F.149, A:P.152 Hydrogen bonds: A:T.142, A:T.142, A:T.144 pi-Stacking: A:H.119

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 4 residues within 4Å: Chain A: Y.73, H.84, A.85, F.86 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.85 GOL.11: 3 residues within 4Å: Chain A: L.82, Y.111, Y.141 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.80, A:Y.141, A:Y.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Spicer, T.P. et al., Characterization of selective exosite-binding inhibitors of matrix metalloproteinase 13 that prevent articular cartilage degradation in vitro. J.Med.Chem. (2014)

Release Date

2014-12-10

Peptides

Collagenase 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Collagenase 3

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