SMTL ID : 4yhf.2 (1 other biounit)

Bruton's tyrosine kinase in complex with a t-butyl cyanoacrylamide inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

15 x NA: SODIUM ION(Non-functional Binders)

NA.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.2: 1 residues within 4Å: Chain A: E.26 No protein-ligand interaction detected (PLIP) NA.4: 5 residues within 4Å: Chain A: L.102, R.144 Ligands: 4C9.3, CL.26, CL.27 No protein-ligand interaction detected (PLIP) NA.5: 4 residues within 4Å: Chain A: S.242, K.244, V.245, V.273 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.242, A:S.242 NA.6: 3 residues within 4Å: Chain A: R.237, S.242, E.243 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.237, A:E.243 Water bridges: A:R.237, A:K.244 NA.7: 3 residues within 4Å: Chain A: K.214, Y.236 Ligands: SO4.23 No protein-ligand interaction detected (PLIP) NA.8: 1 residues within 4Å: Chain A: T.29 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.29 NA.9: 4 residues within 4Å: Chain A: Y.104, F.112, M.120, G.152 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.152 Water bridges: A:V.154 NA.10: 6 residues within 4Å: Chain A: T.114, Y.210, L.240, A.241, S.242, V.245 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.242, A:S.242 Water bridges: A:Y.210 NA.11: 2 residues within 4Å: Chain A: L.233, R.234 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.234, A:R.234 NA.12: 3 residues within 4Å: Chain A: Y.164, V.165, L.166 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.165 NA.13: 3 residues within 4Å: Chain A: P.18, C.83, Q.86 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.86 NA.14: 3 residues within 4Å: Chain A: E.64, V.67, Y.164 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.164, A:Y.164 NA.15: 3 residues within 4Å: Chain A: R.181, T.221, N.222 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.222, A:N.222 Water bridges: A:S.223 NA.16: 4 residues within 4Å: Chain A: E.15, C.83, T.84, K.85 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.84, A:T.84, A:K.85 Water bridges: A:E.15

1 x 4C9: (2S)-2-({(3R)-3-[4-amino-3-(4-phenoxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl}carbonyl)-4,4-dimethylpentanenitrile(Non-covalent)

4C9.3: 27 residues within 4Å: Chain A: L.27, G.28, T.29, G.30, V.35, A.47, K.49, M.68, V.77, L.79, I.91, T.93, E.94, Y.95, M.96, G.99, C.100, L.102, N.103, R.144, L.147, S.157, D.158, F.159, L.161 Ligands: NA.4, CL.26 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.35, A:K.49, A:V.77, A:L.79, A:I.91, A:T.93, A:L.102, A:N.103, A:R.144 Hydrogen bonds: A:T.93, A:E.94, A:M.96, A:C.100 Water bridges: A:N.103 pi-Stacking: A:F.159

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

EDO.17: 12 residues within 4Å: Chain A: R.139, D.140, L.141, P.179, W.182, S.183, P.184, V.187, F.193, S.197, D.198, A.201 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.139, A:R.139, A:L.141, A:L.141, A:S.197 EDO.18: 4 residues within 4Å: Chain A: K.25, L.27, Y.37, Y.95 No protein-ligand interaction detected (PLIP) EDO.19: 4 residues within 4Å: Chain A: L.137, S.194, S.195, K.196 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.195, A:S.195 EDO.20: 5 residues within 4Å: Chain A: A.230, Q.231, G.232, R.234, E.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.230 Water bridges: A:G.232 EDO.21: 10 residues within 4Å: Chain A: W.207, K.214, M.215, P.216, Y.217, E.218, R.219, L.235, Y.236 Ligands: CL.24 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.217, A:E.218 EDO.22: 7 residues within 4Å: Chain A: E.64, Q.135, F.136, L.137, R.139, G.160, R.163 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.135, A:L.137, A:L.137, A:R.139, A:R.139

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.23: 6 residues within 4Å: Chain A: S.211, K.214, Y.236, P.238, H.239 Ligands: NA.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.239 Salt bridges: A:K.214

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

CL.24: 5 residues within 4Å: Chain A: Y.217, F.220, L.233, L.235 Ligands: EDO.21 Ligand excluded by PLIP CL.25: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain A: L.102, R.106 Ligands: 4C9.3, NA.4 Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain A: L.102, R.144, W.182 Ligands: NA.4 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bradshaw, J.M. et al., Prolonged and tunable residence time using reversible covalent kinase inhibitors. Nat.Chem.Biol. (2015)

Release Date

2015-05-13

Peptides

Tyrosine-protein kinase BTK: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Tyrosine-protein kinase BTK

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