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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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)

4C9.1: 24 residues within 4Å: Chain A: L.27, G.28, T.29, 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 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.35, A:A.47, A:K.49, A:V.77, A:L.79, A:L.102, A:N.103, A:R.144, A:L.161 Hydrogen bonds: A:T.93, A:E.94, A:M.96, A:C.100 Water bridges: A:N.103 pi-Stacking: A:F.159

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

NA.2: 4 residues within 4Å: Chain A: R.237, S.242, E.243 Ligands: CL.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.243 NA.3: 3 residues within 4Å: Chain A: Q.116, E.119, M.120 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.116, A:M.120 NA.4: 2 residues within 4Å: Chain A: Y.236, R.237 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.237 NA.5: 2 residues within 4Å: Chain A: Q.116 Ligands: CL.15 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.113, A:Q.116 NA.6: 2 residues within 4Å: Chain A: H.73, E.74 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.74 NA.7: 1 residues within 4Å: Chain A: Y.95 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.95, A:Y.95 NA.8: 7 residues within 4Å: Chain A: E.186, V.187, K.192, F.193, S.194, K.196, S.197 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.186, A:E.186, A:S.197 Water bridges: A:S.194 NA.9: 7 residues within 4Å: Chain A: R.139, D.140, S.162, P.179, F.193 Ligands: EDO.10, CL.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.162 NA.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

EDO.10: 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, A.201 Ligands: NA.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.141 Water bridges: A:R.139, A:D.140, A:L.141, A:S.197 EDO.11: 8 residues within 4Å: Chain A: T.114, Q.115, L.118, Y.210, S.242, V.245, V.273, E.277 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.210, A:Y.210

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

SO4.12: 4 residues within 4Å: Chain A: Y.217, E.218, R.219, Y.236 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.219, A:Y.236, A:Y.236 Water bridges: A:Y.217 Salt bridges: A:R.219 SO4.13: 4 residues within 4Å: Chain A: R.234, W.253, H.254, E.255 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.234, A:E.255 Water bridges: A:R.234, A:H.254, A:H.254 Salt bridges: A:H.254

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

CL.14: 4 residues within 4Å: Chain A: S.242, E.243, K.244 Ligands: NA.2 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain A: H.110, F.112, Q.116 Ligands: NA.5 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain A: R.139, S.162, F.178, F.193 Ligands: NA.9 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
A

Tyrosine-protein kinase BTK

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