SMTL ID : 9dmu.1

Cryo-EM structure of IMPDH2 bound to IMP and GAD

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

8 x IMP: INOSINIC ACID(Non-covalent)

IMP.1: 27 residues within 4Å: Chain A: S.72, P.73, M.74, N.307, R.326, G.332, S.333, I.334, C.335, I.336, T.337, D.368, G.369, G.370, I.371, M.389, M.390, G.391, S.392, Y.415, G.417, M.418, G.419, S.420, Q.445, G.446 Ligands: 01.2 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:S.72, A:N.307, A:R.326, A:S.333, A:S.333, A:D.368, A:G.370, A:G.391, A:S.392, A:S.392, A:S.392, A:Y.415, A:M.418, A:G.419, A:S.420, A:Q.445 Water bridges: A:G.332, A:G.332, A:D.368, A:G.369, A:G.369, A:S.392, A:S.392 IMP.4: 27 residues within 4Å: Chain B: S.72, P.73, M.74, N.307, R.326, G.332, S.333, I.334, C.335, I.336, T.337, D.368, G.369, G.370, I.371, M.389, M.390, G.391, S.392, Y.415, G.417, M.418, G.419, S.420, Q.445, G.446 Ligands: 01.5 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:S.72, B:N.307, B:R.326, B:S.333, B:S.333, B:D.368, B:G.370, B:G.391, B:S.392, B:S.392, B:S.392, B:Y.415, B:M.418, B:G.419, B:S.420, B:Q.445 Water bridges: B:G.332, B:G.332, B:D.368, B:G.369, B:G.369, B:S.392, B:S.392 IMP.7: 27 residues within 4Å: Chain C: S.72, P.73, M.74, N.307, R.326, G.332, S.333, I.334, C.335, I.336, T.337, D.368, G.369, G.370, I.371, M.389, M.390, G.391, S.392, Y.415, G.417, M.418, G.419, S.420, Q.445, G.446 Ligands: 01.8 23 PLIP interactions: 23 interactions with chain C Hydrogen bonds: C:S.72, C:N.307, C:R.326, C:S.333, C:S.333, C:D.368, C:G.370, C:G.391, C:S.392, C:S.392, C:S.392, C:Y.415, C:M.418, C:G.419, C:S.420, C:Q.445 Water bridges: C:G.332, C:G.332, C:D.368, C:G.369, C:I.371, C:S.392, C:S.392 IMP.11: 28 residues within 4Å: Chain C: H.508 Chain D: S.72, P.73, M.74, N.307, R.326, G.332, S.333, I.334, C.335, I.336, T.337, D.368, G.369, G.370, I.371, M.389, M.390, G.391, S.392, Y.415, G.417, M.418, G.419, S.420, Q.445, G.446 Ligands: 01.12 24 PLIP interactions: 24 interactions with chain D Hydrogen bonds: D:S.72, D:N.307, D:R.326, D:S.333, D:S.333, D:D.368, D:G.370, D:G.391, D:S.392, D:S.392, D:S.392, D:Y.415, D:M.418, D:G.419, D:S.420, D:Q.445 Water bridges: D:G.332, D:G.332, D:D.368, D:D.368, D:G.369, D:I.371, D:S.392, D:S.392 IMP.13: 27 residues within 4Å: Chain E: S.72, P.73, M.74, N.307, R.326, G.332, S.333, I.334, C.335, I.336, T.337, D.368, G.369, G.370, I.371, M.389, M.390, G.391, S.392, Y.415, G.417, M.418, G.419, S.420, Q.445, G.446 Ligands: 01.14 24 PLIP interactions: 24 interactions with chain E Hydrogen bonds: E:S.72, E:N.307, E:R.326, E:S.333, E:S.333, E:D.368, E:G.370, E:G.391, E:S.392, E:S.392, E:S.392, E:Y.415, E:M.418, E:G.419, E:S.420, E:Q.445 Water bridges: E:G.332, E:G.332, E:D.368, E:D.368, E:G.369, E:G.369, E:S.392, E:S.392 IMP.16: 27 residues within 4Å: Chain F: S.72, P.73, M.74, N.307, R.326, G.332, S.333, I.334, C.335, I.336, T.337, D.368, G.369, G.370, I.371, M.389, M.390, G.391, S.392, Y.415, G.417, M.418, G.419, S.420, Q.445, G.446 Ligands: 01.17 24 PLIP interactions: 24 interactions with chain F Hydrogen bonds: F:S.72, F:N.307, F:R.326, F:S.333, F:S.333, F:D.368, F:G.370, F:G.391, F:S.392, F:S.392, F:S.392, F:Y.415, F:M.418, F:G.419, F:S.420, F:Q.445 Water bridges: F:G.332, F:G.332, F:D.368, F:D.368, F:G.369, F:G.369, F:S.392, F:S.392 IMP.19: 27 residues within 4Å: Chain G: S.72, P.73, M.74, N.307, R.326, G.332, S.333, I.334, C.335, I.336, T.337, D.368, G.369, G.370, I.371, M.389, M.390, G.391, S.392, Y.415, G.417, M.418, G.419, S.420, Q.445, G.446 Ligands: 01.20 23 PLIP interactions: 23 interactions with chain G Hydrogen bonds: G:S.72, G:N.307, G:R.326, G:S.333, G:S.333, G:D.368, G:G.370, G:G.391, G:S.392, G:S.392, G:S.392, G:Y.415, G:M.418, G:G.419, G:S.420, G:Q.445 Water bridges: G:G.332, G:G.332, G:D.368, G:G.369, G:G.369, G:S.392, G:S.392 IMP.23: 27 residues within 4Å: Chain H: S.72, P.73, M.74, N.307, R.326, G.332, S.333, I.334, C.335, I.336, T.337, D.368, G.369, G.370, I.371, M.389, M.390, G.391, S.392, Y.415, G.417, M.418, G.419, S.420, Q.445, G.446 Ligands: 01.24 24 PLIP interactions: 24 interactions with chain H Hydrogen bonds: H:S.72, H:N.307, H:R.326, H:S.333, H:S.333, H:D.368, H:G.370, H:G.391, H:S.392, H:S.392, H:S.392, H:Y.415, H:M.418, H:G.419, H:S.420, H:Q.445 Water bridges: H:G.332, H:G.332, H:D.368, H:D.368, H:G.369, H:G.369, H:S.392, H:S.392

8 x 01: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-[3-(thiophen-2-ylcarbonylamino)pyridin-1-yl]oxolan-2-yl]methyl hydrogen phosphate

01.2: 18 residues within 4Å: Chain A: H.97, T.256, H.257, D.278, S.279, S.280, F.286, N.307, R.326, M.418, G.419, M.424, Q.445 Chain D: I.46, T.49, H.470, Q.473 Ligands: IMP.1 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:M.418 Hydrogen bonds: A:T.256, A:D.278, A:S.279, A:S.280, A:S.280, D:Q.473 Water bridges: A:T.256, A:T.256, A:T.256, A:S.279 Salt bridges: A:H.257 pi-Stacking: A:H.257, A:F.286, A:F.286 01.5: 18 residues within 4Å: Chain A: I.46, T.49, H.470, Q.473 Chain B: H.97, T.256, H.257, D.278, S.279, S.280, F.286, N.307, R.326, M.418, G.419, M.424, Q.445 Ligands: IMP.4 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:M.418 Hydrogen bonds: B:T.256, B:D.278, B:S.279, B:S.280, B:S.280, A:Q.473 Water bridges: B:T.256, B:T.256, B:T.256, B:S.279 Salt bridges: B:H.257 pi-Stacking: B:H.257, B:F.286, B:F.286 01.8: 18 residues within 4Å: Chain B: I.46, T.49, H.470, Q.473 Chain C: H.97, T.256, H.257, D.278, S.279, S.280, F.286, N.307, R.326, M.418, G.419, M.424, Q.445 Ligands: IMP.7 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:M.418 Hydrogen bonds: C:T.256, C:D.278, C:S.279, C:S.280, C:S.280, B:Q.473 Water bridges: C:T.256, C:T.256, C:T.256, C:S.279 Salt bridges: C:H.257 pi-Stacking: C:H.257, C:F.286, C:F.286 01.12: 18 residues within 4Å: Chain C: I.46, T.49, H.470, Q.473 Chain D: H.97, T.256, H.257, D.278, S.279, S.280, F.286, N.307, R.326, M.418, G.419, M.424, Q.445 Ligands: IMP.11 15 PLIP interactions: 14 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:M.418 Hydrogen bonds: D:T.256, D:D.278, D:S.279, D:S.280, D:S.280, C:Q.473 Water bridges: D:T.256, D:T.256, D:T.256, D:S.279 Salt bridges: D:H.257 pi-Stacking: D:H.257, D:F.286, D:F.286 01.14: 18 residues within 4Å: Chain E: H.97, T.256, H.257, D.278, S.279, S.280, F.286, N.307, R.326, M.418, G.419, M.424, Q.445 Chain H: I.46, T.49, H.470, Q.473 Ligands: IMP.13 16 PLIP interactions: 1 interactions with chain H, 15 interactions with chain E Hydrogen bonds: H:Q.473, E:T.256, E:D.278, E:S.279, E:S.280, E:S.280 Hydrophobic interactions: E:M.418 Water bridges: E:T.256, E:T.256, E:T.256, E:D.278, E:S.279 Salt bridges: E:H.257 pi-Stacking: E:H.257, E:F.286, E:F.286 01.17: 18 residues within 4Å: Chain E: I.46, T.49, H.470, Q.473 Chain F: H.97, T.256, H.257, D.278, S.279, S.280, F.286, N.307, R.326, M.418, G.419, M.424, Q.445 Ligands: IMP.16 16 PLIP interactions: 15 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:M.418 Hydrogen bonds: F:T.256, F:D.278, F:S.279, F:S.280, F:S.280, E:Q.473 Water bridges: F:T.256, F:T.256, F:T.256, F:D.278, F:S.279 Salt bridges: F:H.257 pi-Stacking: F:H.257, F:F.286, F:F.286 01.20: 18 residues within 4Å: Chain F: I.46, T.49, H.470, Q.473 Chain G: H.97, T.256, H.257, D.278, S.279, S.280, F.286, N.307, R.326, M.418, G.419, M.424, Q.445 Ligands: IMP.19 16 PLIP interactions: 15 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: G:M.418 Hydrogen bonds: G:T.256, G:D.278, G:S.279, G:S.280, G:S.280, F:Q.473 Water bridges: G:T.256, G:T.256, G:T.256, G:D.278, G:S.279 Salt bridges: G:H.257 pi-Stacking: G:H.257, G:F.286, G:F.286 01.24: 18 residues within 4Å: Chain G: I.46, T.49, H.470, Q.473 Chain H: H.97, T.256, H.257, D.278, S.279, S.280, F.286, N.307, R.326, M.418, G.419, M.424, Q.445 Ligands: IMP.23 16 PLIP interactions: 15 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:M.418 Hydrogen bonds: H:T.256, H:D.278, H:S.279, H:S.280, H:S.280, G:Q.473 Water bridges: H:T.256, H:T.256, H:T.256, H:D.278, H:S.279 Salt bridges: H:H.257 pi-Stacking: H:H.257, H:F.286, H:F.286

8 x K: POTASSIUM ION(Non-covalent)

K.3: 8 residues within 4Å: Chain A: E.504, G.505, G.506, H.508 Chain B: G.330, S.331, G.332, C.335 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Metal complexes: A:E.504, A:G.505, A:G.506, B:G.332, B:C.335 K.6: 8 residues within 4Å: Chain B: E.504, G.505, G.506, H.508 Chain C: G.330, S.331, G.332, C.335 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Metal complexes: B:E.504, B:G.505, B:G.506, C:G.332, C:C.335 K.9: 8 residues within 4Å: Chain C: E.504, G.505, G.506, H.508 Chain D: G.330, S.331, G.332, C.335 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Metal complexes: D:G.332, D:C.335, C:E.504, C:G.505, C:G.506 K.10: 8 residues within 4Å: Chain A: G.330, S.331, G.332, C.335 Chain D: E.504, G.505, G.506, H.508 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D Metal complexes: A:G.332, A:C.335, D:E.504, D:G.505, D:G.506 K.15: 8 residues within 4Å: Chain E: E.504, G.505, G.506, H.508 Chain F: G.330, S.331, G.332, C.335 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain F Metal complexes: E:E.504, E:G.505, E:G.506, F:G.332, F:C.335 K.18: 8 residues within 4Å: Chain F: E.504, G.505, G.506, H.508 Chain G: G.330, S.331, G.332, C.335 5 PLIP interactions: 2 interactions with chain G, 3 interactions with chain F Metal complexes: G:G.332, G:C.335, F:E.504, F:G.505, F:G.506 K.21: 8 residues within 4Å: Chain G: E.504, G.505, G.506, H.508 Chain H: G.330, S.331, G.332, C.335 5 PLIP interactions: 2 interactions with chain H, 3 interactions with chain G Metal complexes: H:G.332, H:C.335, G:E.504, G:G.505, G:G.506 K.22: 8 residues within 4Å: Chain E: G.330, S.331, G.332, C.335 Chain H: E.504, G.505, G.506, H.508 5 PLIP interactions: 3 interactions with chain H, 2 interactions with chain E Metal complexes: H:E.504, H:G.505, H:G.506, E:G.332, E:C.335

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Y.J. et al., Gliocidin is a nicotinamide-mimetic prodrug that targets glioblastoma. Nature (2024)

Release Date

2024-11-27

Peptides

Inosine-5'-monophosphate dehydrogenase 2: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Inosine-5'-monophosphate dehydrogenase 2