SMTL ID : 8coj.1

Crystal structure of human soluble adenylyl cyclase catalytic domain in complex with the inhibitor TDI-10228

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x VE1: 4-chloranyl-6-[4-[(3-fluorophenyl)methyl]-1-methyl-pyrazol-3-yl]pyrimidin-2-amine(Non-covalent)

VE1.1: 19 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 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.45, 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 Halogen bonds: A:Q.179

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

DMS.2: 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:Y.77 pi-Cation interactions: A:Y.77 DMS.3: 6 residues within 4Å: Chain A: I.88, F.89, F.226, D.227, F.230, Y.240 2 PLIP interactions: 2 interactions with chain A pi-Cation interactions: A:F.89, A:F.230 DMS.4: 11 residues within 4Å: Chain A: L.23, I.24, V.25, Y.26, G.27, H.28, F.29, L.261, S.264, L.265, Y.268 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.29 DMS.5: 5 residues within 4Å: Chain A: N.76, S.80, E.84, 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

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

ACT.6: 7 residues within 4Å: Chain A: T.161, H.162, Q.266, K.267, V.269, E.271, L.274 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.266 Salt bridges: A:H.162

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

EDO.7: 8 residues within 4Å: Chain A: D.22, G.90, G.91, D.92, M.237, Y.239, Y.240, P.241 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.22 EDO.8: 7 residues within 4Å: Chain A: I.88, Y.240, P.241, K.246, N.247, L.248, L.249 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.241 EDO.9: 6 residues within 4Å: Chain A: N.247, L.248, L.249, R.250, C.253, V.400 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.249 EDO.10: 1 residues within 4Å: Chain A: E.7 No protein-ligand interaction detected (PLIP) EDO.11: 7 residues within 4Å: Chain A: L.124, N.185, D.186, V.187, K.214, V.215, N.216 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.187, A:V.187, A:V.215 EDO.12: 7 residues within 4Å: Chain A: K.95, H.164, F.165, I.332, N.333, K.334, V.335 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.95, A:H.164, A:V.335

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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