SMTL ID : 4l19.3 (2 other biounits)

Matrix metalloproteinase-13 complexed with selective inhibitor compound Q1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-tetramer

Ligands

10 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.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.119, A:H.123, A:H.129 ZN.3: 3 residues within 4Å: Chain A: S.147, H.148 Ligands: GOL.9 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.148 ZN.10: 4 residues within 4Å: Chain B: H.69, D.71, H.84, H.97 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.69, B:D.71, B:H.84, B:H.97 ZN.11: 4 residues within 4Å: Chain B: H.119, H.123, H.129 Ligands: FMT.14 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.119, B:H.123, B:H.129 ZN.21: 4 residues within 4Å: Chain C: H.69, D.71, H.84, H.97 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.69, C:D.71, C:H.84, C:H.97 ZN.22: 4 residues within 4Å: Chain C: H.119, H.123, H.129 Ligands: FMT.26 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.119, C:H.123, C:H.129 ZN.23: 3 residues within 4Å: Chain C: S.147, H.148 Ligands: GOL.29 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.148 ZN.30: 4 residues within 4Å: Chain D: H.69, D.71, H.84, H.97 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.69, D:D.71, D:H.84, D:H.97 ZN.31: 4 residues within 4Å: Chain D: H.119, H.123, H.129 Ligands: FMT.34 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.119, D:H.123, D:H.129

8 x CA: CALCIUM ION(Non-covalent)

CA.4: 7 residues within 4Å: Chain A: D.76, G.77, P.78, 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 CA.5: 5 residues within 4Å: Chain A: D.59, N.91, Y.92, 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.1, H2O.3 CA.12: 4 residues within 4Å: Chain B: D.59, N.91, G.93, D.95 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.59, B:N.91, B:G.93, B:D.95, H2O.8, H2O.9 CA.13: 6 residues within 4Å: Chain B: D.76, G.77, S.79, L.81, D.99, E.102 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:D.76, B:G.77, B:S.79, B:L.81, B:D.99, B:E.102 CA.24: 7 residues within 4Å: Chain C: D.76, G.77, P.78, S.79, L.81, D.99, E.102 6 PLIP interactions: 6 interactions with chain C Metal complexes: C:D.76, C:G.77, C:S.79, C:L.81, C:D.99, C:E.102 CA.25: 5 residues within 4Å: Chain C: D.59, N.91, Y.92, G.93, D.95 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.59, C:N.91, C:G.93, C:D.95, H2O.11, H2O.13 CA.32: 4 residues within 4Å: Chain D: D.59, N.91, G.93, D.95 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.59, D:N.91, D:G.93, D:D.95, H2O.18, H2O.19 CA.33: 6 residues within 4Å: Chain D: D.76, G.77, S.79, L.81, D.99, E.102 6 PLIP interactions: 6 interactions with chain D Metal complexes: D:D.76, D:G.77, D:S.79, D:L.81, D:D.99, D:E.102

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

FMT.6: 7 residues within 4Å: Chain A: A.83, H.119, E.120, H.123, H.129 Ligands: ZN.2, 1UA.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.83 FMT.14: 6 residues within 4Å: Chain B: A.83, H.119, E.120, H.123, H.129 Ligands: ZN.11 No protein-ligand interaction detected (PLIP) FMT.15: 4 residues within 4Å: Chain B: T.27, H.28 Chain C: T.27, H.28 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:H.28, C:H.28 Water bridges: B:T.27, B:S.29, C:S.29 FMT.16: 1 residues within 4Å: Chain B: K.131 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.131 FMT.17: 3 residues within 4Å: Chain B: K.12, M.13, N.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.13, B:N.14, B:N.14 FMT.26: 7 residues within 4Å: Chain C: A.83, H.119, E.120, H.123, H.129 Ligands: ZN.22, 1UA.28 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.83 FMT.34: 6 residues within 4Å: Chain D: A.83, H.119, E.120, H.123, H.129 Ligands: ZN.31 No protein-ligand interaction detected (PLIP) FMT.35: 4 residues within 4Å: Chain A: T.27, H.28 Chain D: T.27, H.28 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:H.28, D:H.28 Water bridges: A:S.29, D:T.27, D:S.29 FMT.36: 1 residues within 4Å: Chain D: K.131 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.131 FMT.37: 3 residues within 4Å: Chain D: K.12, M.13, N.14 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:M.13, D:N.14, D:N.14

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

1UA.7: 12 residues within 4Å: Chain A: L.115, 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:T.144, A:F.149, A:P.152 Hydrogen bonds: A:T.142, A:T.142, A:T.144 pi-Stacking: A:H.119 1UA.8: 5 residues within 4Å: Chain A: Y.73, A.85, F.86, H.123 Ligands: FMT.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.73 Water bridges: A:A.85 pi-Stacking: A:F.86 1UA.18: 13 residues within 4Å: Chain B: 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 B Hydrophobic interactions: B:H.119, B:Y.141, B:F.149, B:P.152 Hydrogen bonds: B:T.142, B:T.142, B:T.144 pi-Stacking: B:H.119 1UA.27: 12 residues within 4Å: Chain C: L.115, H.119, G.134, L.136, F.138, P.139, I.140, Y.141, T.142, T.144, F.149, P.152 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:H.119, C:T.144, C:F.149, C:P.152 Hydrogen bonds: C:T.142, C:T.144 pi-Stacking: C:H.119 1UA.28: 5 residues within 4Å: Chain C: Y.73, A.85, F.86, H.123 Ligands: FMT.26 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.73 Water bridges: C:A.85 pi-Stacking: C:F.86 1UA.38: 13 residues within 4Å: Chain D: 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 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:H.119, D:Y.141, D:F.149, D:P.152 Hydrogen bonds: D:T.142, D:T.144 Water bridges: D:T.142, D:T.142 pi-Stacking: D:H.119

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 3 residues within 4Å: Chain A: S.147, H.148 Ligands: ZN.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.147 GOL.19: 4 residues within 4Å: Chain B: Y.73, H.84, A.85, F.86 1 PLIP interactions: 1 interactions with chain B Water bridges: B:A.85 GOL.20: 3 residues within 4Å: Chain B: L.82, Y.111, Y.141 3 PLIP interactions: 3 interactions with chain B Water bridges: B:G.80, B:Y.141, B:Y.141 GOL.29: 3 residues within 4Å: Chain C: S.147, H.148 Ligands: ZN.23 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.147 GOL.39: 4 residues within 4Å: Chain D: Y.73, H.84, A.85, F.86 1 PLIP interactions: 1 interactions with chain D Water bridges: D:A.85 GOL.40: 3 residues within 4Å: Chain D: L.82, Y.111, Y.141 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.111 Water bridges: D:G.80, D:Y.141, D: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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Collagenase 3

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