SMTL ID : 5iv4.1

Crystal structure of the human soluble adenylyl cyclase in complex with the allosteric inhibitor LRE1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

monomer

Ligands

1 x LRI: 6-chloro-N~4~-cyclopropyl-N~4~-[(thiophen-2-yl)methyl]pyrimidine-2,4-diamine(Non-covalent)

LRI.1: 14 residues within 4Å: Chain A: F.45, L.94, K.95, A.97, L.102, F.165, L.166, V.167, V.172, V.175, R.176, F.336, M.337, F.338 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.45, A:K.95, A:K.95, A:A.97, A:L.102, A:R.176, A:F.336, A:F.336 Hydrogen bonds: A:V.167, A:M.337, A:M.337 pi-Stacking: A:F.45

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

ACT.2: 2 residues within 4Å: Chain A: Q.283, G.284 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.283 Water bridges: A:S.287 ACT.3: 6 residues within 4Å: Chain A: K.95, H.164, N.333, K.334, V.335 Ligands: GOL.15 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.335 Water bridges: A:K.95, A:S.163, A:F.165 Salt bridges: A:K.95, A:H.164

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

EDO.4: 3 residues within 4Å: Chain A: I.390, Q.409, K.410 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.390, A:I.390 Water bridges: A:K.410, A:K.410 EDO.5: 3 residues within 4Å: Chain A: I.88, N.247, L.249 No protein-ligand interaction detected (PLIP) EDO.6: 3 residues within 4Å: Chain A: F.230, T.231, T.234 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.234 Water bridges: A:Y.240, A:S.242 EDO.7: 5 residues within 4Å: Chain A: P.31, R.33, G.158, D.159, E.160 No protein-ligand interaction detected (PLIP) EDO.8: 8 residues within 4Å: Chain A: N.298, F.336, M.337, F.338, G.341, C.342, S.343, M.419 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.298, A:N.298, A:F.336, A:F.338, A:S.343 Water bridges: A:G.341, A:S.343

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

DMS.9: 5 residues within 4Å: Chain A: Y.77, H.78, A.81, L.129, F.130 No protein-ligand interaction detected (PLIP) DMS.10: 4 residues within 4Å: Chain A: I.88, F.89, F.226, F.230 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.227 pi-Cation interactions: A:F.89, A:F.230 DMS.11: 6 residues within 4Å: Chain A: I.24, G.27, H.28, F.29, L.261, 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.12: 3 residues within 4Å: Chain A: S.80, H.398, T.399 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.399 pi-Cation interactions: A:H.398

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.13: 2 residues within 4Å: Chain A: G.408, Q.409 Ligand excluded by PLIP

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.14: 9 residues within 4Å: Chain A: H.162, H.164, Y.318, T.322, L.325, K.326, G.330, Q.331, I.332 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.164, A:Y.318 Water bridges: A:L.325, A:G.330

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 8 residues within 4Å: Chain A: H.19, L.20, K.95, F.165, Y.268, K.334, E.403 Ligands: ACT.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.19, A:K.334 Water bridges: A:K.334, A:Y.404, A:Y.404

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ramos-Espiritu, L. et al., Discovery of LRE1 as a specific and allosteric inhibitor of soluble adenylyl cyclase. Nat.Chem.Biol. (2016)

Release Date

2016-08-17

Peptides

Adenylate cyclase type 10: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Adenylate cyclase type 10

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