SMTL ID : 9byj.1

Crystal Structure of Hck in complex with the Src-family kinase inhibitor A-419259

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x VSE: 7-[trans-4-(4-methylpiperazin-1-yl)cyclohexyl]-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine(Non-covalent)

VSE.1: 19 residues within 4Å: Chain A: L.196, V.204, A.216, K.218, M.237, V.246, I.259, T.261, E.262, F.263, M.264, S.268, D.271, L.316, A.326, D.327, F.328 Ligands: SCN.11, SCN.15 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.196, A:V.204, A:V.204, A:K.218, A:V.246, A:L.316, A:L.316, A:A.326 Hydrogen bonds: A:T.261, A:E.262, A:M.264 Salt bridges: A:D.271, A:D.271 pi-Stacking: A:F.328

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

EDO.2: 7 residues within 4Å: Chain A: G.199, Q.200, F.201, G.202, K.218, D.327 Ligands: SCN.15 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.200, A:F.201, A:G.202, A:K.218, A:D.327 EDO.7: 5 residues within 4Å: Chain A: Y.305, I.306, R.308, G.329, R.332 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.306, A:R.308 EDO.8: 5 residues within 4Å: Chain A: F.263, M.264, A.265, S.318, A.319 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.265, A:A.319 EDO.14: 6 residues within 4Å: Chain A: R.311, A.313, N.314, D.327 Ligands: SCN.11, SCN.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.314, A:D.327 EDO.23: 9 residues within 4Å: Chain A: M.237, K.238, L.240, Q.241, L.245, V.246, K.247, L.248, F.328 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.248 EDO.24: 5 residues within 4Å: Chain A: G.223, M.225, S.226, E.255 Ligands: SCN.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.337

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

DMS.3: 6 residues within 4Å: Chain A: P.354, I.357, N.358, I.395, L.398, E.399 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.358 Water bridges: A:N.424 Salt bridges: A:E.399 DMS.22: 5 residues within 4Å: Chain A: D.336, A.345, K.346, F.347 Ligands: SCN.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.346 Water bridges: A:F.347 Salt bridges: A:D.336

15 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.4: 6 residues within 4Å: Chain A: Y.17, I.20, H.21, W.42, K.176, P.177 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.212 SCN.5: 1 residues within 4Å: Chain A: E.408 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.408 SCN.6: 3 residues within 4Å: Chain A: D.181, W.183, E.184 No protein-ligand interaction detected (PLIP) SCN.9: 5 residues within 4Å: Chain A: H.242, E.295, A.298, F.299, Q.436 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.299, A:Q.436 SCN.10: 3 residues within 4Å: Chain A: G.223, E.255 Ligands: EDO.24 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.223 SCN.11: 8 residues within 4Å: Chain A: V.204, K.218, A.313, N.314, D.327 Ligands: VSE.1, EDO.14, SCN.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.218 SCN.12: 5 residues within 4Å: Chain A: E.335, D.336, T.340, G.344 Ligands: DMS.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.340 SCN.13: 7 residues within 4Å: Chain A: H.21, H.22, E.23, D.24, W.42, E.179, K.180 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.180 SCN.15: 8 residues within 4Å: Chain A: G.199, G.202, V.204, K.218 Ligands: VSE.1, EDO.2, SCN.11, EDO.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.199 SCN.16: 2 residues within 4Å: Chain A: S.275, D.276 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.276 Water bridges: A:E.277 SCN.17: 1 residues within 4Å: Chain A: G.401 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.403 SCN.18: 2 residues within 4Å: Chain A: A.341, R.342 No protein-ligand interaction detected (PLIP) SCN.19: 3 residues within 4Å: Chain A: S.142, T.143, F.144 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.143 SCN.20: 2 residues within 4Å: Chain A: P.282, P.284 No protein-ligand interaction detected (PLIP) SCN.21: 7 residues within 4Å: Chain A: K.80, I.287, D.288, L.439, D.440, F.442, Y.443 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.80, A:D.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Selzer, A.M. et al., Cocrystallization of the Src-Family Kinase Hck with the ATP-Site Inhibitor A-419259 Stabilizes an Extended Activation Loop Conformation. Biochemistry (2024)

Release Date

2024-10-09

Peptides

Tyrosine-protein kinase HCK: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Tyrosine-protein kinase HCK