SMTL ID : 4x20.1

Discovery of cytotoxic Dolastatin 10 analogs with N-terminal modifications

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

hetero-2-2-1-mer

Ligands

2 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 23 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, I.16, D.69, E.71, D.98, S.140, G.143, G.144, T.145, G.146, P.173, V.177, S.178, E.183, N.206, Y.224, N.228, I.231 Chain B: K.252 Ligands: MG.2 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:E.71, A:E.71, A:D.98, A:S.140, A:G.144, A:T.145, A:G.146, A:S.178, A:E.183, A:N.206, A:N.228, A:N.228 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252, B:K.252 GTP.6: 26 residues within 4Å: Chain C: V.9, G.10, Q.11, A.12, Q.15, I.16, D.69, E.71, D.98, N.101, S.140, G.143, G.144, T.145, G.146, I.171, V.177, S.178, E.183, N.206, Y.224, N.228, I.231 Chain D: N.247, K.252 Ligands: MG.7 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.11, C:A.12, C:E.71, C:E.71, C:S.140, C:T.145, C:T.145, C:G.146, C:V.177, C:E.183, C:N.206, C:N.206, C:N.228, C:N.228 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: D.98, A.99, A.100, G.144, T.145 Chain B: K.252 Ligands: GTP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.145 MG.7: 6 residues within 4Å: Chain C: D.98, A.99, N.101, G.144, T.145 Ligands: GTP.6 No protein-ligand interaction detected (PLIP)

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.3: 19 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, P.171, V.175, S.176, E.181, N.204, Y.222, L.225, N.226 Ligands: 3WY.5 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:Q.11, B:C.12, B:S.138, B:G.142, B:T.143, B:T.143, B:G.144, B:S.176, B:S.176, B:E.181, B:N.204, B:N.204, B:N.226, B:N.226 pi-Stacking: B:Y.222, B:Y.222 GDP.8: 18 residues within 4Å: Chain D: A.9, G.10, Q.11, C.12, Q.15, S.138, G.140, G.141, G.142, T.143, G.144, P.171, V.175, E.181, N.204, Y.222, N.226 Ligands: 3WY.10 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:S.138, D:G.142, D:T.143, D:T.143, D:T.143, D:T.143, D:G.144, D:E.181, D:N.204, D:N.204, D:N.226, D:N.226 pi-Stacking: D:Y.222, D:Y.222

2 x LOC: N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide(Non-covalent)

LOC.4: 22 residues within 4Å: Chain A: S.178, T.179, A.180, V.181 Chain B: C.239, L.240, L.246, A.248, D.249, K.252, L.253, N.256, M.257, T.312, V.313, A.314, V.316, N.348, K.350, T.351, A.352, I.368 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.248, B:K.252, B:L.253, B:L.253, B:K.350, B:K.350 Hydrogen bonds: A:V.181 LOC.9: 19 residues within 4Å: Chain C: S.178, T.179, A.180, V.181 Chain D: L.240, L.246, A.248, D.249, K.252, L.253, N.256, M.257, T.312, V.313, A.314, V.316, N.348, K.350, I.368 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.246, D:K.252, D:L.253, D:L.253, D:K.350 Hydrogen bonds: D:K.350, C:T.179, C:V.181

2 x 3WY: 2-methyl-L-prolyl-N-[(3R,4S,5S)-1-{(2S)-2-[(1R,2R)-3-{[(1S)-1-carboxy-2-phenylethyl]amino}-1-methoxy-2-methyl-3-oxopropyl]pyrrolidin-1-yl}-3-methoxy-5-methyl-1-oxoheptan-4-yl]-N-methyl-L-valinamide(Non-covalent)

3WY.5: 16 residues within 4Å: Chain B: Q.15, K.174, V.175, D.177, Y.208, T.219, P.220, T.221, Y.222, G.223, R.276 Chain C: A.247, N.249, P.325, N.329 Ligands: GDP.3 16 PLIP interactions: 12 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:Q.15, B:V.175, B:V.175, B:Y.208, B:T.221, B:Y.222, C:P.325, C:P.325 Hydrogen bonds: B:D.177, B:T.221, B:Y.222, B:G.223, B:R.276, C:N.329, C:N.329 Salt bridges: B:R.276 3WY.10: 12 residues within 4Å: Chain D: Q.11, Q.15, P.173, K.174, V.175, D.177, Y.208, P.220, T.221, Y.222, G.223 Ligands: GDP.8 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:Q.11, D:Q.15, D:Y.208, D:Y.222, D:Y.222 Hydrogen bonds: D:T.221, D:Y.222, D:G.223

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maderna, A. et al., Discovery of cytotoxic dolastatin 10 analogues with N-terminal modifications. J.Med.Chem. (2014)

Release Date

2015-03-25

Peptides

Tubulin alpha chain: AC
Tubulin beta chain: BD
Stathmin-4: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

Tubulin alpha chain

Tubulin beta chain

Stathmin-4

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