SMTL ID : 8cot.1

Complex of human soluble adenylyl cyclase 10 catalytic core with inhibitor TDI-10962

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x VBB: 2-(dimethylamino)ethyl 5-(2-azanyl-6-chloranyl-pyrimidin-4-yl)-2-methyl-4-(phenylmethyl)pyrazole-3-carboxylate(Non-covalent)

VBB.1: 17 residues within 4Å: Chain A: F.45, K.95, F.96, A.97, D.99, A.100, L.101, L.102, F.165, L.166, V.167, V.172, V.175, R.176, F.336, M.337, F.338 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.45, A:K.95, A:L.102, A:V.172, A:V.175, A:R.176, A:F.336, A:F.336, A:F.338, A:F.338 Hydrogen bonds: A:V.167, A:M.337, A:M.337 Salt bridges: A:D.99

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

DMS.2: 6 residues within 4Å: Chain A: I.24, G.27, F.29, L.261, S.264, Y.268 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.264 pi-Cation interactions: A:F.29 DMS.3: 3 residues within 4Å: Chain A: S.80, H.398, T.399 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.399, A:T.399 pi-Cation interactions: A:H.398 DMS.4: 3 residues within 4Å: Chain A: I.88, F.89, F.230 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:D.227 pi-Cation interactions: A:F.89, A:F.230 DMS.7: 5 residues within 4Å: Chain A: Y.77, H.78, A.81, L.129, F.130 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.78 pi-Cation interactions: A:Y.77

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

EDO.5: 7 residues within 4Å: Chain A: T.55, E.56, L.289, I.390, F.392, G.408, Q.409 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.390, A:Q.409 Water bridges: A:K.410 EDO.9: 6 residues within 4Å: Chain A: D.22, G.90, G.91, M.237, Y.239, Y.240 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.22 Water bridges: A:G.90, A:L.104, A:Y.239 EDO.12: 3 residues within 4Å: Chain A: I.202, E.203, I.204 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.202, A:I.204 EDO.14: 6 residues within 4Å: Chain A: F.370, S.374, I.379, Q.380, T.381, V.382 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.374, A:V.382, A:V.382

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 6 residues within 4Å: Chain A: I.88, Y.240, P.241, K.246, L.248, L.249 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.249 ACT.8: 5 residues within 4Å: Chain A: K.95, H.164, N.333, K.334, V.335 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.333, A:V.335 Water bridges: A:K.95 Salt bridges: A:K.95, A:H.164 ACT.10: 5 residues within 4Å: Chain A: N.298, F.338, G.341, S.343, M.419 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.338 Hydrogen bonds: A:N.298, A:F.338, A:G.341, A:S.343 ACT.11: 4 residues within 4Å: Chain A: L.255, K.256, D.258, L.261 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.258 Hydrogen bonds: A:K.256 ACT.13: 4 residues within 4Å: Chain A: T.322, G.330, Q.331, I.332 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.322, A:G.330, A:I.332 Water bridges: A:H.162 Salt bridges: A:H.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sun, S. et al., Scaffold Hopping and Optimization of Small Molecule Soluble Adenyl Cyclase Inhibitors Led by Free Energy Perturbation. J.Chem.Inf.Model. (2023)

Release Date

2023-04-26

Peptides

Adenylate cyclase type 10: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Adenylate cyclase type 10

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