SMTL ID : 4gr9.1

Synthesis of novel MT3 receptor ligands via unusual Knoevenagel condensation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.173, H.177, C.222 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.173, A:H.177, A:C.222, A:C.222 ZN.4: 4 residues within 4Å: Chain B: H.173, H.177, C.222, T.223 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.173, B:H.177, B:C.222, B:C.222

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.2: 26 residues within 4Å: Chain A: H.11, K.15, S.16, F.17, N.18, S.20, P.102, L.103, Y.104, W.105, F.106, T.147, T.148, G.149, G.150, Y.155, P.192, E.193, E.197, R.200, K.201 Chain B: N.66, Y.67, G.68, D.117 Ligands: 372.7 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.104, A:Y.104, A:Y.104, A:Y.104, B:Y.67 Hydrogen bonds: A:F.17, A:N.18, A:N.18, A:S.20, A:S.20, A:L.103, A:W.105, A:F.106, A:T.147, A:T.147, A:G.149, A:G.150, A:Y.155, A:R.200, B:N.66 Salt bridges: A:H.11 pi-Stacking: A:F.17 FAD.6: 24 residues within 4Å: Chain A: N.66, Y.67, G.68, D.117 Chain B: H.11, K.15, S.16, F.17, N.18, S.20, P.102, L.103, Y.104, W.105, F.106, T.147, T.148, G.149, G.150, Y.155, E.193, R.200, K.201 Ligands: 372.3 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.104, B:Y.104, B:Y.104, A:Y.67 Hydrogen bonds: B:F.17, B:N.18, B:N.18, B:S.20, B:S.20, B:L.103, B:L.103, B:W.105, B:F.106, B:T.147, B:T.147, B:G.149, B:G.150, B:Y.155, B:Y.155 Salt bridges: B:H.11 pi-Stacking: B:F.17

2 x 372: N-[(3R)-3-(cyanomethyl)-1-methyl-2-oxo-2,3-dihydro-1H-indol-5-yl]acetamide(Non-covalent)

372.3: 13 residues within 4Å: Chain A: G.68, Q.122, F.126, G.174, F.178 Chain B: W.105, F.106, G.149, G.150, M.154, Y.155, N.161 Ligands: FAD.6 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.126, A:F.178 Hydrogen bonds: B:N.161 pi-Stacking: B:W.105 372.7: 12 residues within 4Å: Chain A: W.105, F.106, G.149, G.150, Y.155, N.161 Chain B: G.68, Q.122, F.126, G.174, F.178 Ligands: FAD.2 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.161 pi-Stacking: A:W.105 Hydrophobic interactions: B:F.126, B:F.178, B:F.178

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: E.47, R.49 Chain B: N.45, E.47, R.49 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:N.45, B:R.49, B:R.49, A:E.47, A:R.49, A:R.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Volkova, M.S. et al., Synthesis of novel МТ3 receptor ligands via an unusual Knoevenagel condensation. Bioorg.Med.Chem.Lett. (2012)

Release Date

2013-07-10

Peptides

Ribosyldihydronicotinamide dehydrogenase [quinone]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribosyldihydronicotinamide dehydrogenase [quinone]

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