SMTL ID : 8cnh.1

Crystal structure of human soluble adenylyl cyclase (sAC) in complex with inhibitor TDI-10512

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x V6U: methyl 2-[[3-(2-azanyl-6-chloranyl-pyrimidin-4-yl)-1-methyl-pyrazol-4-yl]methyl]benzoate(Non-covalent)

V6U.1: 20 residues within 4Å: Chain A: F.45, L.94, K.95, F.96, A.97, A.100, L.101, L.102, F.165, L.166, V.167, I.168, V.172, V.175, R.176, Q.179, F.336, M.337, F.338 Ligands: EDO.11 13 PLIP interactions: 13 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 Hydrogen bonds: A:V.167, A:M.337, A:M.337 Salt bridges: A:R.176

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

DMS.2: 5 residues within 4Å: Chain A: I.88, F.89, F.226, D.227, F.230 2 PLIP interactions: 2 interactions with chain A pi-Cation interactions: A:F.89, A:F.230 DMS.3: 7 residues within 4Å: Chain A: I.24, G.27, H.28, F.29, S.264, L.265, Y.268 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.27, A:F.29 pi-Cation interactions: A:F.29 DMS.4: 4 residues within 4Å: Chain A: N.76, 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.6: 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 DMS.12: 8 residues within 4Å: Chain A: I.88, Y.240, P.241, H.245, K.246, N.247, L.248, L.249 No protein-ligand interaction detected (PLIP)

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

EDO.5: 8 residues within 4Å: Chain A: L.124, H.127, N.185, D.186, V.187, K.214, V.215, N.216 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.187, A:V.187 EDO.7: 8 residues within 4Å: Chain A: T.161, H.162, Q.266, K.267, V.269, M.270, E.271, L.274 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.266, A:V.269 EDO.8: 6 residues within 4Å: Chain A: P.356, D.357, E.358, L.359, G.434, N.436 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.357, A:L.359 EDO.9: 9 residues within 4Å: Chain A: H.162, H.164, Y.318, T.322, L.325, K.326, G.330, Q.331, I.332 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.164, A:Y.318, A:I.332 EDO.10: 11 residues within 4Å: Chain A: N.298, M.300, F.336, M.337, F.338, D.339, G.341, C.342, S.343, M.418, M.419 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.298, A:S.343, A:S.343 EDO.11: 9 residues within 4Å: Chain A: F.45, A.97, D.99, A.100, F.296, F.336, F.338, S.343 Ligands: V6U.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.99 EDO.14: 9 residues within 4Å: Chain A: T.55, E.56, S.59, L.289, I.390, V.391, 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.15: 7 residues within 4Å: Chain A: I.13, T.254, L.255, K.256, P.257, D.258, L.261 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.254, A:K.256 EDO.16: 8 residues within 4Å: Chain A: D.22, G.90, G.91, D.92, M.237, Y.239, Y.240, P.241 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.22, A:D.22

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

ACT.13: 5 residues within 4Å: Chain A: D.22, L.23, Y.26, R.106, Y.239 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.106, A:R.106 Salt bridges: A:R.106

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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