SMTL ID : 6gwr.1

Structure of the kinase domain of human DDR1 in complex with a potent and selective inhibitor of DDR1 and DDR2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-dimer

Ligands

2 x FEW: 3-(2-imidazo[1,2-a]pyrazin-3-ylethynyl)-~{N}-[3-[(4-methylpiperazin-1-yl)methyl]-5-(trifluoromethyl)phenyl]-4-propan-2-yl-benzamide(Non-covalent)

FEW.1: 23 residues within 4Å: Chain A: V.26, A.55, V.56, K.57, E.74, I.77, M.78, L.81, I.86, I.87, M.101, T.103, D.104, Y.105, M.106, F.164, H.166, L.175, I.184, A.185, D.186, F.187 Ligands: EDO.12 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.26, A:E.74, A:I.87, A:L.175, A:D.186, A:F.187 Hydrogen bonds: A:E.74, A:E.74, A:M.106, A:D.186 Salt bridges: A:E.74, A:D.186, A:D.186 FEW.16: 21 residues within 4Å: Chain B: V.26, A.55, V.56, K.57, E.74, I.77, M.78, L.81, I.86, I.87, M.101, T.103, D.104, Y.105, M.106, F.164, H.166, L.175, A.185, D.186, F.187 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.26, B:A.55, B:E.74, B:T.103, B:L.175, B:D.186 Hydrogen bonds: B:E.74, B:E.74, B:M.106, B:D.186 Salt bridges: B:E.74, B:D.186, B:D.186

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

SO4.2: 4 residues within 4Å: Chain A: S.190, R.191, N.192, L.193 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.192, A:L.193 SO4.3: 6 residues within 4Å: Chain A: H.147, A.150, Q.151, S.154, H.304, A.308 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.150, A:S.154 Salt bridges: A:H.147, A:H.304 SO4.4: 2 residues within 4Å: Chain A: R.157, R.305 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.157, A:R.157 Salt bridges: A:R.157, A:R.305 SO4.5: 5 residues within 4Å: Chain A: R.274, P.276, A.277 Chain B: G.203, R.204 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.277, B:R.204 Salt bridges: A:R.274, B:R.204 SO4.17: 4 residues within 4Å: Chain B: R.274, P.276, A.277, C.278 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.277, B:C.278 Salt bridges: B:R.274 SO4.18: 4 residues within 4Å: Chain B: W.236, F.247, L.272, S.273 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.247, B:S.273 Water bridges: B:G.248, B:G.248

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

EDO.6: 9 residues within 4Å: Chain A: W.236, Q.245, P.246, F.247, G.248, L.272, S.273 Chain B: K.73 Ligands: EDO.13 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.245, A:F.247, A:G.248, A:S.273, A:S.273 EDO.7: 5 residues within 4Å: Chain A: W.229, F.247, Y.271, L.272, W.290 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.272 Water bridges: A:R.210, A:W.229, A:N.258 EDO.8: 4 residues within 4Å: Chain A: R.268 Chain B: L.72, V.75, K.76 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.268 Water bridges: A:R.268, B:S.79, B:S.79 EDO.9: 4 residues within 4Å: Chain A: R.80, L.162, N.163, F.164 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.80 EDO.10: 3 residues within 4Å: Chain A: L.72, V.75, K.76 No protein-ligand interaction detected (PLIP) EDO.11: 1 residues within 4Å: Chain A: R.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.13 EDO.12: 5 residues within 4Å: Chain A: L.18, G.19, V.26, F.187 Ligands: FEW.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.18 EDO.13: 4 residues within 4Å: Chain A: W.236, M.240, S.273 Ligands: EDO.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.273 EDO.14: 3 residues within 4Å: Chain A: Y.142, A.277, P.279 No protein-ligand interaction detected (PLIP) EDO.15: 4 residues within 4Å: Chain A: M.189, A.195, Y.198, R.200 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.196, A:Y.198 EDO.19: 6 residues within 4Å: Chain B: W.229, F.247, V.270, Y.271, L.272, W.290 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.272 Water bridges: B:W.229, B:N.258 EDO.20: 3 residues within 4Å: Chain B: E.257, E.261, R.268 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.257, B:E.261, B:E.261 EDO.21: 4 residues within 4Å: Chain B: M.189, A.195, Y.198, R.200 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.196, B:Y.198 EDO.22: 4 residues within 4Å: Chain B: G.196, R.210, Q.245, D.252 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.245, B:D.252 Water bridges: B:R.210, B:D.252 EDO.23: 3 residues within 4Å: Chain A: M.240 Chain B: Q.202, A.205 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.202

Links

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Citation

Wang, Z. et al., Design, Synthesis, and Biological Evaluation of 3-(Imidazo[1,2- a]pyrazin-3-ylethynyl)-4-isopropyl- N-(3-((4-methylpiperazin-1-yl)methyl)-5-(trifluoromethyl)phenyl)benzamide as a Dual Inhibitor of Discoidin Domain Receptors 1 and 2. J. Med. Chem. (2018)

Release Date

2018-08-08

Peptides

Epithelial discoidin domain-containing receptor 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Epithelial discoidin domain-containing receptor 1

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