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SMTL ID : 4p5d.2
(1 other biounit)
CRYSTAL STRUCTURE OF RAT DNPH1 (RCL) WITH 6-NAPHTHYL-PURINE-RIBOSIDE-MONOPHOSPHATE
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 2.11 Å
Oligo State
homo-dimer
Ligands
2 x
N6P
:
6-(naphthalen-2-yl)-9-(5-O-phosphono-beta-D-ribofuranosyl)-9H-purine
(Non-covalent)
N6P.1:
23 residues within 4Å:
Chain A:
Y.6
,
C.8
,
G.9
,
S.10
,
I.11
,
R.12
,
G.13
,
H.38
,
V.39
,
E.45
,
E.49
,
E.50
,
A.51
,
I.58
,
N.62
,
S.80
,
L.81
,
G.82
,
V.83
,
E.86
Chain B:
S.110
,
A.111
,
M.112
17
PLIP interactions
:
16 interactions with chain A
,
1 interactions with chain B
Hydrophobic interactions:
A:E.45
,
A:E.50
,
A:E.50
Hydrogen bonds:
A:Y.6
,
A:Y.6
,
A:G.9
,
A:S.10
,
A:I.11
,
A:R.12
,
A:G.13
,
A:N.62
,
A:S.80
,
A:G.82
,
A:V.83
,
B:S.110
Water bridges:
A:L.81
,
A:L.81
N6P.3:
23 residues within 4Å:
Chain A:
S.110
,
A.111
,
M.112
Chain B:
Y.6
,
C.8
,
G.9
,
S.10
,
I.11
,
R.12
,
G.13
,
H.38
,
V.39
,
E.45
,
E.49
,
E.50
,
A.51
,
I.58
,
N.62
,
S.80
,
L.81
,
G.82
,
V.83
,
E.86
16
PLIP interactions
:
15 interactions with chain B
,
1 interactions with chain A
Hydrophobic interactions:
B:E.45
,
B:E.50
,
B:E.50
Hydrogen bonds:
B:Y.6
,
B:G.9
,
B:S.10
,
B:I.11
,
B:R.12
,
B:G.13
,
B:N.62
,
B:S.80
,
B:G.82
,
B:V.83
,
A:S.110
Water bridges:
B:L.81
,
B:L.81
2 x
SO4
:
SULFATE ION
(Non-functional Binders)
SO4.2:
2 residues within 4Å:
Chain A:
R.27
,
R.30
4
PLIP interactions
:
4 interactions with chain A
Water bridges:
A:R.27
,
A:R.27
Salt bridges:
A:R.27
,
A:R.30
SO4.4:
2 residues within 4Å:
Chain B:
R.27
,
R.30
4
PLIP interactions
:
4 interactions with chain B
Water bridges:
B:R.27
,
B:R.27
Salt bridges:
B:R.27
,
B:R.30
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Amiable, C. et al., 6-(Hetero)Arylpurine nucleotides as inhibitors of the oncogenic target DNPH1: Synthesis, structural studies and cytotoxic activities. Eur.J.Med.Chem. (2014)
Release Date
2014-08-20
Peptides
2'-deoxynucleoside 5'-phosphate N-hydrolase 1:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
A
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2'-deoxynucleoside 5'-phosphate N-hydrolase 1
Toggle Identical (AB)
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|
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4p5d.1
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