SMTL ID : 2zb2.1

Human liver glycogen phosphorylase a complexed with glcose and 5-chloro-N-[4-(1,2-dihydroxyethyl)phenyl]-1H-indole-2-carboxamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

2 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.1: 13 residues within 4Å: Chain A: G.137, G.138, L.139, L.142, N.287, H.380, V.458, N.487, Y.576, E.675, A.676, S.677, G.678 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:L.139, A:N.287, A:N.287, A:H.380, A:Y.576, A:E.675, A:A.676, A:S.677, A:S.677, A:G.678 Water bridges: A:E.675, A:E.675, A:T.679 GLC.5: 14 residues within 4Å: Chain B: G.137, G.138, L.139, L.142, N.287, H.380, V.458, N.487, Y.576, E.675, A.676, S.677, G.678, T.679 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:L.139, B:N.287, B:N.287, B:N.287, B:N.487, B:E.675, B:S.677, B:G.678, B:G.678 Water bridges: B:A.676, B:A.676, B:T.679 Salt bridges: B:H.380

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.2: 8 residues within 4Å: Chain A: Q.74, Y.78, R.84, Y.158, F.199, R.245, D.309, R.313 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.74, A:Y.158, A:R.245, A:R.245, A:R.313 Salt bridges: A:R.84, A:R.313 MES.6: 7 residues within 4Å: Chain A: V.48 Chain B: Q.74, Q.75, Y.78, R.196, F.199 Ligands: MPD.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.74, B:Q.75, B:R.196, B:R.196 Water bridges: B:R.245

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.3: 15 residues within 4Å: Chain A: Y.93, G.137, G.138, W.494, K.571, K.577, Y.651, R.652, V.653, A.656, E.675, G.678, T.679, G.680, K.683 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.93, A:Y.651, A:K.683 Hydrogen bonds: A:V.570, A:T.679, A:G.680 Water bridges: A:K.571, A:G.678, A:T.679 Salt bridges: A:K.571, A:K.577 PLP.7: 15 residues within 4Å: Chain B: Y.93, G.137, G.138, W.494, K.571, K.577, Y.651, R.652, V.653, A.656, E.675, G.678, T.679, G.680, K.683 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.93, B:Y.651, B:V.653, B:K.683 Hydrogen bonds: B:T.679, B:G.680 Water bridges: B:Y.93, B:G.137, B:K.571, B:K.571, B:K.577 Salt bridges: B:K.571, B:K.577

2 x A46: 5-chloro-N-{4-[(1R)-1,2-dihydroxyethyl]phenyl}-1H-indole-2-carboxamide(Non-covalent)

A46.4: 16 residues within 4Å: Chain A: R.63, L.66, V.67, W.70, P.191, W.192, E.193, K.194, P.232 Chain B: T.41, V.43, F.56, H.60, Y.188, G.189, P.191 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:W.70, A:K.194, A:P.232, B:T.41, B:V.43 Hydrogen bonds: A:E.193, B:T.41, B:H.60, B:Y.188 Water bridges: A:R.63, A:R.63, A:K.194 pi-Cation interactions: A:R.63 A46.8: 17 residues within 4Å: Chain A: T.41, L.42, V.43, F.56, H.60, Y.188, G.189, P.191 Chain B: R.63, L.66, V.67, W.70, P.191, W.192, E.193, K.194, P.232 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:T.41, A:L.42, A:V.43, B:W.70, B:K.194, B:P.232 Hydrogen bonds: A:T.41, A:H.60, A:Y.188, B:E.193 Water bridges: B:K.194 pi-Cation interactions: B:R.63

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

MPD.9: 7 residues within 4Å: Chain A: V.43, V.48 Chain B: W.70, I.71, Q.74, R.196 Ligands: MES.6 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.70, B:W.70, B:Q.74, B:Q.74, A:V.43 Hydrogen bonds: B:R.196, A:V.43 Water bridges: B:Q.74, B:D.230 MPD.10: 6 residues within 4Å: Chain A: W.70, Q.74, R.196 Chain B: V.43, K.44, V.48 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.70, A:Q.74 Hydrogen bonds: A:D.230, B:V.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Onda, K. et al., Synthesis of 5-chloro-N-aryl-1H-indole-2-carboxamide derivatives as inhibitors of human liver glycogen phosphorylase a. Bioorg.Med.Chem. (2008)

Release Date

2008-09-02

Peptides

Glycogen phosphorylase, liver form: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycogen phosphorylase, liver form