SMTL ID : 3wzd.1

KDR in complex with ligand lenvatinib

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

monomer

Ligands

1 x LEV: 4-{3-chloro-4-[(cyclopropylcarbamoyl)amino]phenoxy}-7-methoxyquinoline-6-carboxamide(Non-covalent)

LEV.1: 21 residues within 4Å: Chain A: L.27, G.28, V.35, A.53, K.55, E.72, I.75, L.76, V.86, V.103, E.104, F.105, C.106, K.107, G.109, L.172, C.182, D.183, F.184, L.186 Ligands: GOL.10 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.27, A:A.53, A:E.72, A:I.75, A:L.76, A:L.76, A:F.184 Hydrogen bonds: A:G.28, A:E.72, A:E.72, A:E.72, A:C.106, A:D.183

4 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.2: 4 residues within 4Å: Chain A: I.75, C.161, I.162, G.185 No protein-ligand interaction detected (PLIP) DTT.3: 4 residues within 4Å: Chain A: D.39, C.49, R.50, T.51 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.51 DTT.4: 6 residues within 4Å: Chain A: I.214, F.215, D.249, E.250, C.253, R.254 No protein-ligand interaction detected (PLIP) DTT.5: 4 residues within 4Å: Chain A: C.144, F.147, L.301 Ligands: SO4.11 No protein-ligand interaction detected (PLIP)

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

EDO.6: 4 residues within 4Å: Chain A: F.108, T.113, Y.114, S.117 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.113, A:S.117 Water bridges: A:K.107, A:F.108 EDO.7: 6 residues within 4Å: Chain A: A.157, I.221, Q.222, T.289, F.290, S.291 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.290, A:S.291, A:S.291 EDO.8: 4 residues within 4Å: Chain A: W.233, S.237, P.265, D.266 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.266 Water bridges: A:D.266 EDO.9: 6 residues within 4Å: Chain A: F.108, L.173, S.174, E.175, K.176, N.177 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.174, A:N.177 Water bridges: A:Y.114, A:K.176, A:N.177

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 7 residues within 4Å: Chain A: G.28, R.169, N.170, L.172, C.182, D.183 Ligands: LEV.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.169, A:D.183

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

SO4.11: 5 residues within 4Å: Chain A: E.140, H.141, C.144, N.177 Ligands: DTT.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.140, A:N.177 Salt bridges: A:H.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Okamoto, K. et al., Distinct binding mode of multikinase inhibitor lenvatinib revealed by biochemical characterization. ACS MED.CHEM.LETT. (2015)

Release Date

2015-05-27

Peptides

Vascular endothelial growth factor receptor 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Vascular endothelial growth factor receptor 2

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