SMTL ID : 5n3v.1

Thermolysin in complex with inhibitor JC292

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.12 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.142, H.146, Y.157, E.166, H.231 Ligands: 8L5.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.142, A:H.146, A:E.166, A:E.166

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: D.57, D.59, Q.61 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.57, A:Q.61, H2O.4, H2O.4, H2O.11 CA.3: 8 residues within 4Å: Chain A: D.138, E.177, D.185, E.187, I.188, G.189, E.190 Ligands: CA.4 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.138, A:E.177, A:E.177, A:D.185, A:E.190 CA.4: 6 residues within 4Å: Chain A: E.177, N.183, P.184, D.185, E.190 Ligands: CA.3 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.177, A:N.183, A:D.185, A:E.190, H2O.2, H2O.3 CA.5: 4 residues within 4Å: Chain A: Y.193, T.194, I.197, D.200 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.193, A:I.197, A:D.200, H2O.5, H2O.10

1 x 8L5: N-(aminomethyl)-N~2~-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucinamide(Non-covalent)

8L5.6: 20 residues within 4Å: Chain A: N.112, A.113, F.114, W.115, N.116, F.130, L.133, V.139, H.142, E.143, H.146, Y.157, E.166, I.188, G.189, L.202, R.203, H.231 Ligands: ZN.1, MPD.7 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.114, A:L.133, A:V.139, A:L.202 Hydrogen bonds: A:N.112, A:N.112, A:E.143, A:Y.157, A:R.203, A:R.203, A:H.231 Water bridges: A:N.112, A:N.112, A:W.115, A:E.143

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.7: 4 residues within 4Å: Chain A: Y.110, N.112, F.114 Ligands: 8L5.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.114 Hydrogen bonds: A:Y.110 Water bridges: A:Y.110, A:N.112 MPD.8: 3 residues within 4Å: Chain A: S.298, T.299, K.307 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.299 Water bridges: A:K.307, A:K.307

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.9: 1 residues within 4Å: Chain A: Y.66 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.66 DMS.10: 5 residues within 4Å: Chain A: I.1, T.2, G.3, Q.31, N.33 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.3 DMS.11: 4 residues within 4Å: Chain A: G.259, R.260, D.261, K.262 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.260, A:D.261 Water bridges: A:K.262 Salt bridges: A:D.261

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cramer, J. et al., Paying the Price of Desolvation in Solvent-Exposed Protein Pockets: Impact of Distal Solubilizing Groups on Affinity and Binding Thermodynamics in a Series of Thermolysin Inhibitors. J. Med. Chem. (2017)

Release Date

2017-06-21

Peptides

Thermolysin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

Thermolysin

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