SMTL ID : 6npu.1

C-abl Kinase domain with the activator(cmpd29), N-(1-(3,4-dichlorophenyl)-4,5-dihydro-1H-pyrazol-3-yl)acetamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

homo-dimer

Ligands

2 x STI: 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE(Non-covalent)

STI.1: 22 residues within 4Å: Chain A: L.34, Y.39, V.42, A.55, V.56, K.57, E.72, V.75, M.76, I.79, V.85, I.99, T.101, F.103, M.104, F.145, I.146, H.147, L.156, A.166, D.167, F.168 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.34, A:L.34, A:Y.39, A:A.55, A:V.85, A:I.99, A:T.101, A:L.156, A:D.167, A:F.168 Hydrogen bonds: A:E.72, A:T.101, A:T.101, A:M.104, A:D.167 pi-Stacking: A:Y.39 STI.4: 20 residues within 4Å: Chain B: L.34, Y.39, V.42, A.55, V.56, K.57, E.72, V.75, M.76, I.79, V.85, I.99, T.101, F.103, M.104, I.146, H.147, A.166, D.167, F.168 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.34, B:Y.39, B:V.42, B:A.55, B:K.57, B:I.79, B:I.99, B:D.167, B:F.168 Hydrogen bonds: B:E.72, B:T.101, B:M.104, B:D.167 pi-Stacking: B:Y.39

2 x KWV: ~{N}-[2-(3,4-dichlorophenyl)-3,4-dihydropyrazol-5-yl]ethanamide(Non-covalent)

KWV.2: 15 residues within 4Å: Chain A: R.118, A.123, L.126, L.127, A.130, L.215, I.218, A.219, Y.221, E.248, G.249, C.250, P.251, V.254, F.279 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.126, A:A.219, A:Y.221, A:P.251, A:V.254 Hydrogen bonds: A:A.219 Halogen bonds: A:L.215 KWV.7: 14 residues within 4Å: Chain B: A.123, L.126, L.127, A.130, L.215, I.218, A.219, Y.221, E.248, G.249, C.250, P.251, V.254, F.279 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.126, B:L.127, B:A.219, B:Y.221, B:P.251 Hydrogen bonds: B:A.219 Halogen bonds: B:L.215

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

SO4.3: 1 residues within 4Å: Chain B: K.80 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.80

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain B: D.241, R.243, R.259, W.262 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.241, B:R.259, B:W.262 Water bridges: B:R.243 GOL.6: 5 residues within 4Å: Chain B: L.238, E.239, D.241, R.243, W.264 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:L.238, B:D.241, B:D.241, B:R.243, B:R.243 Water bridges: B:W.264, B:W.264

1 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.8: 3 residues within 4Å: Chain B: Y.199, K.201, P.266 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.201

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Simpson, G.L. et al., Identification and Optimization of Novel Small c-Abl Kinase Activators Using Fragment and HTS Methodologies. J. Med. Chem. (2019)

Release Date

2019-03-13

Peptides

Tyrosine-protein kinase ABL1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tyrosine-protein kinase ABL1

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