SMTL ID : 4hma.1

Crystal structure of an MMP twin carboxylate based inhibitor LC20 in complex with the MMP-9 catalytic domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.117, H.121, H.127 Ligands: 0ZD.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.117, A:H.121, A:H.127 ZN.2: 4 residues within 4Å: Chain A: H.66, D.68, H.81, H.94 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.66, A:D.68, A:D.68, A:H.81, A:H.94 ZN.18: 4 residues within 4Å: Chain B: H.117, H.121, H.127 Ligands: 0ZD.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.117, B:H.121, B:H.127 ZN.19: 4 residues within 4Å: Chain B: H.66, D.68, H.81, H.94 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.66, B:D.68, B:H.81, B:H.94

6 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.56, G.88, Q.90, D.92 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.56, A:G.88, A:Q.90, A:D.92, H2O.2, H2O.2 CA.4: 6 residues within 4Å: Chain A: D.73, G.74, D.76, L.78, D.96, E.99 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.73, A:G.74, A:D.76, A:L.78, A:D.96, A:E.99 CA.5: 5 residues within 4Å: Chain A: S.20, D.22, D.97, E.99, W.101 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.22, A:D.97, A:D.97, A:E.99 CA.20: 4 residues within 4Å: Chain B: D.56, G.88, Q.90, D.92 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.56, B:G.88, B:Q.90, B:D.92, H2O.8, H2O.8 CA.21: 6 residues within 4Å: Chain B: D.73, G.74, D.76, L.78, D.96, E.99 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:D.73, B:G.74, B:D.76, B:L.78, B:D.96, B:E.99 CA.22: 3 residues within 4Å: Chain B: D.22, D.97, E.99 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.22, B:D.97, B:D.97, B:E.99, H2O.11

1 x 0ZD: N,N'-bis(2-[(biphenyl-4ylsulfonyl)[(2R)-1-hydroxy-3-methyl-1-oxobutan-2-yl]-amino]ethyl)benzene-1,3-dicarboxamide(Non-covalent)

0ZD.6: 33 residues within 4Å: Chain A: L.78, L.79, A.80, H.81, L.113, V.114, H.117, Q.118, H.121, H.127, L.134, Y.136, P.137, M.138, Y.139 Chain B: L.78, L.79, A.80, L.113, V.114, H.117, Q.118, H.121, H.127, L.134, Y.136, P.137, M.138, Y.139 Ligands: ZN.1, GOL.7, ZN.18, MLT.23 27 PLIP interactions: 12 interactions with chain B, 15 interactions with chain A Hydrophobic interactions: B:L.78, B:V.114, B:H.117, B:P.137, B:Y.139, A:H.81, A:V.114, A:H.117, A:P.137, A:P.137, A:Y.139 Hydrogen bonds: B:L.79, B:A.80, B:Q.118, A:L.79, A:A.80, A:A.80, A:Q.118 Salt bridges: B:H.117, B:H.121, B:H.127, A:H.117, A:H.121, A:H.127 pi-Stacking: B:H.117, A:H.117 Water bridges: A:P.137

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: Y.70, L.78, H.81 Chain B: P.131, Y.136 Ligands: 0ZD.6 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.136, A:H.81 GOL.8: 4 residues within 4Å: Chain A: F.1, N.153, G.154, H.157 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.150, A:N.153 GOL.9: 1 residues within 4Å: Ligands: PEG.14 No protein-ligand interaction detected (PLIP) GOL.24: 2 residues within 4Å: Ligands: GOL.25, PEG.29 No protein-ligand interaction detected (PLIP) GOL.25: 1 residues within 4Å: Ligands: GOL.24 No protein-ligand interaction detected (PLIP)

6 x PGO: S-1,2-PROPANEDIOL(Non-covalent)(Non-functional Binders)

PGO.10: 5 residues within 4Å: Chain A: E.2, L.5, P.84, G.124, D.126 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.2, A:E.2, A:G.124 Water bridges: A:F.1, A:L.5, A:L.5 PGO.11: 1 residues within 4Å: Chain A: D.98 No protein-ligand interaction detected (PLIP) PGO.12: 3 residues within 4Å: Chain A: G.106, G.108, Y.109 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.109 Hydrogen bonds: A:G.106, A:G.108 PGO.26: 5 residues within 4Å: Chain B: T.142, G.144, P.145, H.148 Ligands: MLT.23 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.142, B:H.148 Water bridges: B:T.142 PGO.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PGO.28: 1 residues within 4Å: Chain B: S.129 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.129

7 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.13: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.90, A:Q.90 PEG.14: 3 residues within 4Å: Chain A: D.68, Y.70 Ligands: GOL.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.70 PEG.15: 2 residues within 4Å: Chain A: F.47, T.48 1 PLIP interactions: 1 interactions with chain A Water bridges: A:F.47 PEG.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PEG.17: 2 residues within 4Å: Chain A: K.75, L.100 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.75 Water bridges: A:G.108 PEG.29: 1 residues within 4Å: Ligands: GOL.24 No protein-ligand interaction detected (PLIP) PEG.30: 4 residues within 4Å: Chain B: D.150, N.153, G.154, H.157 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.150

1 x MLT: D-MALATE(Non-covalent)

MLT.23: 10 residues within 4Å: Chain B: E.132, A.133, L.134, R.140, T.142, P.145, P.146, H.148 Ligands: 0ZD.6, PGO.26 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.145 Water bridges: B:E.132 Salt bridges: B:H.148

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Antoni, C. et al., Crystallization of bi-functional ligand protein complexes. J.Struct.Biol. (2013)

Release Date

2013-04-24

Peptides

Matrix metalloproteinase-9: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Matrix metalloproteinase-9

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