SMTL ID : 5ac2.1

human aldehyde dehydrogenase 1A1 with duocarmycin analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

4 x K9P: 1-[(1S)-1-methyl-5-oxidanyl-1,2-dihydrobenzo[e]indol-3-yl]hexan-1-one(Covalent)

K9P.1: 11 residues within 4Å: Chain A: F.171, M.175, W.178, F.290, H.293, G.294, Y.297, C.302, I.304, Y.457, G.458 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.171, A:W.178, A:H.293, A:Y.297, A:I.304 pi-Stacking: A:F.171 K9P.6: 11 residues within 4Å: Chain B: F.171, M.175, W.178, F.290, H.293, G.294, Y.297, C.302, I.304, Y.457, G.458 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.171, B:W.178, B:H.293, B:Y.297, B:I.304 pi-Stacking: B:F.171 K9P.11: 11 residues within 4Å: Chain C: F.171, M.175, W.178, F.290, H.293, G.294, Y.297, C.302, I.304, Y.457, G.458 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.171, C:W.178, C:H.293, C:Y.297, C:I.304 pi-Stacking: C:F.171 K9P.16: 11 residues within 4Å: Chain D: F.171, M.175, W.178, F.290, H.293, G.294, Y.297, C.302, I.304, Y.457, G.458 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.171, D:W.178, D:H.293, D:Y.297, D:I.304 pi-Stacking: D:F.171

12 x YB: YTTERBIUM (III) ION(Non-covalent)(Non-functional Binders)

YB.2: 1 residues within 4Å: Chain A: D.283 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.283 YB.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.5: 2 residues within 4Å: Chain A: E.249 Ligands: TXE.3 5 PLIP interactions: 1 Ligand-Ligand interactions, 4 Ligand-Water interactions Metal complexes: TXE.3, H2O.4, H2O.4, H2O.5, H2O.7 YB.7: 1 residues within 4Å: Chain B: D.283 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.283 YB.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.10: 2 residues within 4Å: Chain B: E.249 Ligands: TXE.8 5 PLIP interactions: 1 Ligand-Ligand interactions, 4 Ligand-Water interactions Metal complexes: TXE.8, H2O.10, H2O.10, H2O.12, H2O.13 YB.12: 1 residues within 4Å: Chain C: D.283 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.283 YB.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.15: 2 residues within 4Å: Chain C: E.249 Ligands: TXE.13 5 PLIP interactions: 1 Ligand-Ligand interactions, 4 Ligand-Water interactions Metal complexes: TXE.13, H2O.17, H2O.17, H2O.18, H2O.20 YB.17: 1 residues within 4Å: Chain D: D.283 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.283 YB.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.20: 2 residues within 4Å: Chain D: E.249 Ligands: TXE.18 5 PLIP interactions: 1 Ligand-Ligand interactions, 4 Ligand-Water interactions Metal complexes: TXE.18, H2O.23, H2O.23, H2O.24, H2O.26

4 x TXE: [[(2R,3S,4R,5R)-5-[(3R)-3-aminocarbonyl-3,4-dihydro-2H-pyridin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanidyl-ph osphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphate(Non-covalent)

TXE.3: 29 residues within 4Å: Chain A: I.166, I.167, P.168, W.169, N.170, K.193, P.194, A.195, E.196, Y.225, G.226, P.227, G.230, A.231, F.244, T.245, G.246, S.247, V.250, E.269, L.270, G.271, C.303, E.349, Q.350, K.353, E.400, F.402 Ligands: YB.5 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:P.168, A:W.169, A:F.402, A:F.402 Hydrogen bonds: A:N.170, A:N.170, A:K.193, A:P.194, A:G.246, A:S.247, A:S.247, A:S.247, A:Q.350, A:K.353, A:E.400, A:E.400 Water bridges: A:E.196, A:G.226, A:C.303 TXE.8: 29 residues within 4Å: Chain B: I.166, I.167, P.168, W.169, N.170, K.193, P.194, A.195, E.196, Y.225, G.226, P.227, G.230, A.231, F.244, T.245, G.246, S.247, V.250, E.269, L.270, G.271, C.303, E.349, Q.350, K.353, E.400, F.402 Ligands: YB.10 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:P.168, B:W.169, B:F.402, B:F.402 Hydrogen bonds: B:N.170, B:N.170, B:K.193, B:P.194, B:G.246, B:S.247, B:S.247, B:S.247, B:Q.350, B:K.353, B:E.400 Water bridges: B:E.196, B:G.226, B:E.249, B:E.249, B:C.303 TXE.13: 29 residues within 4Å: Chain C: I.166, I.167, P.168, W.169, N.170, K.193, P.194, A.195, E.196, Y.225, G.226, P.227, G.230, A.231, F.244, T.245, G.246, S.247, V.250, E.269, L.270, G.271, C.303, E.349, Q.350, K.353, E.400, F.402 Ligands: YB.15 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:P.168, C:W.169, C:F.402, C:F.402 Hydrogen bonds: C:N.170, C:N.170, C:K.193, C:P.194, C:G.246, C:S.247, C:S.247, C:S.247, C:Q.350, C:K.353, C:E.400 Water bridges: C:E.196, C:G.226, C:E.249, C:E.249, C:C.303 TXE.18: 29 residues within 4Å: Chain D: I.166, I.167, P.168, W.169, N.170, K.193, P.194, A.195, E.196, Y.225, G.226, P.227, G.230, A.231, F.244, T.245, G.246, S.247, V.250, E.269, L.270, G.271, C.303, E.349, Q.350, K.353, E.400, F.402 Ligands: YB.20 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:P.168, D:W.169, D:F.402, D:F.402 Hydrogen bonds: D:N.170, D:N.170, D:K.193, D:P.194, D:G.246, D:S.247, D:S.247, D:S.247, D:Q.350, D:K.353, D:E.400, D:E.400 Water bridges: D:E.196, D:G.226, D:C.303

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koch, M.F. et al., Structural, Biochemical, and Computational Studies Reveal the Mechanism of Selective Aldehyde Dehydrogenase 1A1 Inhibition by Cytotoxic Duocarmycin Analogues. Angew.Chem.Int.Ed.Engl. (2015)

Release Date

2015-08-26

Peptides

RETINAL DEHYDROGENASE 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

RETINAL DEHYDROGENASE 1

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