- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- monomer
- Ligands
- 1 x V9E: 4-chloranyl-6-[1-methyl-4-(thiophen-2-ylmethyl)pyrazol-3-yl]pyrimidin-2-amine
- 4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
DMS.2: 7 residues within 4Å:- Chain A: I.88, F.89, F.226, D.227, F.230, Y.240
- Ligands: PG4.12
2 PLIP interactions:2 interactions with chain A- pi-Cation interactions: A:F.89, A:F.230
DMS.3: 9 residues within 4Å:- Chain A: I.24, V.25, G.27, H.28, F.29, L.261, S.264, L.265, Y.268
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:F.29
- Water bridges: A:S.264
- 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.8: 5 residues within 4Å:- Chain A: Y.77, H.78, A.81, L.129, F.130
1 PLIP interactions:1 interactions with chain A- pi-Cation interactions: A:Y.77
- 5 x ACT: ACETATE ION(Non-functional Binders)
ACT.5: 8 residues within 4Å:- Chain A: K.95, H.164, F.165, I.332, N.333, K.334, V.335
- Ligands: ACT.14
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.6: 3 residues within 4Å:- Chain A: Q.283, G.284, S.287
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:Q.283
- Hydrogen bonds: A:Q.283, A:S.287
ACT.14: 9 residues within 4Å:- Chain A: H.19, L.20, Y.268, V.269, K.334, R.401, E.403, Y.404
- Ligands: ACT.5
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:E.403
- Water bridges: A:H.19, A:E.403
- Salt bridges: A:K.334
ACT.15: 2 residues within 4Å:- Chain A: M.419, Y.420
No protein-ligand interaction detected (PLIP)ACT.16: 6 residues within 4Å:- Chain A: N.223, F.224, N.225, E.228, F.229, K.232
1 PLIP interactions:1 interactions with chain A- Salt bridges: A:K.232
- 6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.7: 7 residues within 4Å:- Chain A: H.164, T.322, L.325, K.326, G.330, Q.331, I.332
7 PLIP interactions:7 interactions with chain A- Hydrogen bonds: A:I.332
- Water bridges: A:H.162, A:H.164, A:T.322, A:L.325, A:G.330, A:I.332
EDO.9: 7 residues within 4Å:- Chain A: F.370, S.374, I.379, Q.380, T.381, V.382, G.423
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:I.379, A:V.382, A:V.382
EDO.10: 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.11: 8 residues within 4Å:- Chain A: M.181, A.182, Q.183, D.186, I.188, E.205, V.207, K.214
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:K.214
EDO.13: 7 residues within 4Å:- Chain A: P.31, R.33, G.158, D.159, E.160, Q.315, M.319
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:E.160
- Water bridges: A:P.31
EDO.17: 8 residues within 4Å:- Chain A: D.10, V.14, R.15, A.18, C.253, T.399, V.400, H.402
1 PLIP interactions:1 interactions with chain A- Water bridges: A:H.402
- 1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
- 1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 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
- 2024-01-03
- Peptides
- Adenylate cyclase type 10: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- monomer
- Ligands
- 1 x V9E: 4-chloranyl-6-[1-methyl-4-(thiophen-2-ylmethyl)pyrazol-3-yl]pyrimidin-2-amine
- 4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- 5 x ACT: ACETATE ION(Non-functional Binders)
- 6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
- 1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 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
- 2024-01-03
- Peptides
- Adenylate cyclase type 10: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A