SMTL ID : 9rhw.2 (2 other biounits)

M. tuberculosis meets European Lead Factory: identification and structural characterization of novel Rv0183 inhibitors using X-ray crystallography: ELF1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-dimer

Ligands

2 x 7WW: [5-(2-chlorophenyl)-1-(4-methoxyphenyl)pyrazol-3-yl]-[(3R)-3-oxidanylpyrrolidin-1-yl]methanone(Non-covalent)

7WW.1: 25 residues within 4Å: Chain A: G.66, L.67, E.69, R.73, H.137, S.138, M.139, A.164, A.167, L.170, V.171, Q.192, E.193, L.194, I.199, Y.209, V.220, I.224, G.225, L.228, R.255, L.256, I.257, H.284, E.285 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.67, A:A.167, A:L.170, A:Q.192, A:V.220, A:L.256, A:L.256 Hydrogen bonds: A:L.67, A:H.137, A:M.139, A:Q.192 7WW.10: 25 residues within 4Å: Chain B: G.66, L.67, E.69, R.73, H.137, S.138, M.139, A.164, A.167, L.170, V.171, Q.192, E.193, L.194, I.199, Y.209, V.220, I.224, G.225, L.228, R.255, L.256, I.257, H.284, E.285 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.67, B:A.167, B:L.170, B:Q.192, B:V.220, B:L.256, B:L.256 Hydrogen bonds: B:L.67, B:H.137, B:S.138, B:M.139, B:Q.192, B:E.285

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 4 residues within 4Å: Chain A: Q.168, G.232, E.233, P.236 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.168 PO4.11: 4 residues within 4Å: Chain B: Q.168, G.232, E.233, P.236 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.168

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

MPD.3: 4 residues within 4Å: Chain A: R.201, D.202, P.203, P.290 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.290 MPD.9: 13 residues within 4Å: Chain A: V.174, V.175, A.178, L.189, P.190, V.191 Chain B: V.175, A.178, L.189, P.190, V.191, R.219 Ligands: MPD.18 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.189, B:P.190, A:V.174 MPD.12: 4 residues within 4Å: Chain B: R.201, D.202, P.203, P.290 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.290 MPD.18: 13 residues within 4Å: Chain A: V.175, A.178, L.189, P.190, V.191, R.219 Chain B: V.174, V.175, A.178, L.189, P.190, V.191 Ligands: MPD.9 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.189, A:P.190, B:V.174

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

DMS.4: 5 residues within 4Å: Chain A: R.73, H.76, V.205, A.208, N.288 No protein-ligand interaction detected (PLIP) DMS.13: 5 residues within 4Å: Chain B: R.73, H.76, V.205, A.208, N.288 No protein-ligand interaction detected (PLIP)

6 x EOH: ETHANOL(Non-functional Binders)

EOH.5: 6 residues within 4Å: Chain A: P.57, E.126, Y.127, P.128, G.129, C.130 No protein-ligand interaction detected (PLIP) EOH.6: 2 residues within 4Å: Chain A: A.272, V.274 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.274 EOH.8: 4 residues within 4Å: Chain A: P.128, G.129, C.130, K.131 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.156 EOH.14: 6 residues within 4Å: Chain B: P.57, E.126, Y.127, P.128, G.129, C.130 No protein-ligand interaction detected (PLIP) EOH.15: 2 residues within 4Å: Chain B: A.272, V.274 1 PLIP interactions: 1 interactions with chain B Water bridges: B:V.274 EOH.17: 4 residues within 4Å: Chain B: P.128, G.129, C.130, K.131 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.156

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 5 residues within 4Å: Chain A: R.201, P.280, G.281, L.282, E.291 No protein-ligand interaction detected (PLIP) EDO.16: 5 residues within 4Å: Chain B: R.201, P.280, G.281, L.282, E.291 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.291

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Riegler-Berket, L. et al., M. tuberculosis meets European Lead Factory: identification and structural characterization of novel Rv0183 inhibitors using X-ray crystallography: ELF1. To Be Published

Release Date

2025-08-13

Peptides

Monoacylglycerol lipase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Monoacylglycerol lipase

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