SMTL ID : 5uwm.1 (1 other biounit)

Matrix metalloproteinase-13 complexed with selective inhibitor compound (R)-17a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

monomer

Ligands

1 x VAL- THR- PRO- LEU- ASN: Collagenase 3(Non-covalent)

VAL-THR-PRO-LEU-ASN.1: 14 residues within 4Å: Chain A: Y.74, L.82, A.84, H.85, A.86, F.87, P.88, H.120, E.121, H.124, D.129, H.130 Ligands: ZN.2, 8OA.7 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.74, A:H.85, A:F.87, A:F.87, A:P.88 Hydrogen bonds: A:Y.74, A:A.84, A:A.86, A:A.86, A:E.121 Water bridges: A:Y.74 Salt bridges: A:H.120, A:H.124, A:H.130

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.120, H.124, H.130 Ligands: VAL-THR-PRO-LEU-ASN.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.120, A:H.124, A:H.130 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

3 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain A: D.77, G.78, S.80, L.82, D.100, E.103 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.77, A:G.78, A:S.80, A:L.82, A:D.100, A:E.103 CA.5: 3 residues within 4Å: Chain A: 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:D.101, H2O.4, H2O.5 CA.6: 5 residues within 4Å: Chain A: D.60, N.92, Y.93, G.94, D.96 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.60, A:N.92, A:G.94, A:D.96, H2O.1, H2O.2

1 x 8OA: (R)-N-(3-methyl-1-(methylamino)-1-oxobutan-2-yl)-5-(4-(((4-oxo-4,5,6,7-tetrahydro-3H-cyclopenta[d]pyrimidin-2-yl)thio)methyl)phenyl)furan-2-carboxamide(Non-covalent)

8OA.7: 20 residues within 4Å: Chain A: G.81, L.82, L.83, A.84, L.116, V.117, H.120, E.121, G.135, L.137, F.139, P.140, I.141, Y.142, T.143, Y.144, T.145, F.150, P.153 Ligands: VAL-THR-PRO-LEU-ASN.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.83, A:V.117, A:H.120, A:F.150, A:P.153 Hydrogen bonds: A:L.83, A:A.84, A:P.140, A:T.143, A:T.145 Water bridges: A:P.140 pi-Stacking: A:H.120

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
A

Collagenase 3

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