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SMTL ID : 7ppg.2
(1 other biounit)
CRYSTAL STRUCTURE OF NAMPT IN COMPLEX WITH COMPOUND 9
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 2.13 Å
Oligo State
homo-dimer
Ligands
4 x
PO4
:
PHOSPHATE ION
(Non-functional Binders)
PO4.1:
5 residues within 4Å:
Chain A:
R.41
,
R.393
,
C.398
,
S.399
,
K.401
8
PLIP interactions
:
7 interactions with chain A
,
1 interactions with chain B
Hydrogen bonds:
A:S.399
,
A:K.416
Water bridges:
A:R.41
,
A:K.424
,
B:R.197
Salt bridges:
A:R.41
,
A:R.393
,
A:K.401
PO4.2:
7 residues within 4Å:
Chain A:
R.197
,
E.247
,
H.248
,
R.312
,
D.314
Chain B:
Y.19
Ligands:
7YX.3
11
PLIP interactions
:
9 interactions with chain A
,
2 interactions with chain B
Hydrogen bonds:
A:H.248
,
B:Y.19
Water bridges:
A:R.197
,
A:R.197
,
A:R.197
,
A:E.247
,
A:S.249
,
B:K.401
Salt bridges:
A:R.197
,
A:H.248
,
A:R.312
PO4.5:
4 residues within 4Å:
Chain A:
R.393
,
D.394
Chain B:
G.384
,
G.385
6
PLIP interactions
:
3 interactions with chain B
,
3 interactions with chain A
Hydrogen bonds:
B:G.384
,
B:G.385
Water bridges:
B:G.386
,
A:R.393
,
A:R.393
Salt bridges:
A:R.393
PO4.6:
5 residues within 4Å:
Chain B:
R.41
,
R.393
,
S.399
,
K.401
,
K.416
14
PLIP interactions
:
12 interactions with chain B
,
2 interactions with chain A
Hydrogen bonds:
B:S.399
Water bridges:
B:R.393
,
B:F.400
,
B:K.401
,
B:K.401
,
B:K.416
,
B:K.416
,
B:K.416
,
A:R.197
,
A:R.197
Salt bridges:
B:R.41
,
B:R.393
,
B:K.401
,
B:K.416
2 x
7YX
:
N-[4-[(4R)-1-cyclopentyl-4-methyl-6-oxidanylidene-4,5-dihydropyridazin-3-yl]phenyl]-1,3-dihydropyrrolo[3,4-c]pyridine-2-carboxamide
(Non-covalent)
7YX.3:
16 residues within 4Å:
Chain A:
Y.189
,
H.192
,
F.194
,
R.197
,
D.220
,
Y.241
,
S.242
,
V.243
,
A.245
,
S.276
,
R.312
,
I.352
,
A.380
Chain B:
D.17
,
Y.19
Ligands:
PO4.2
12
PLIP interactions
:
11 interactions with chain A
,
1 interactions with chain B
Hydrophobic interactions:
A:Y.189
,
A:D.220
,
A:Y.241
,
A:V.243
,
A:I.352
,
A:A.380
Hydrogen bonds:
A:S.276
Water bridges:
A:D.220
,
A:D.220
,
A:R.312
pi-Stacking:
A:F.194
,
B:Y.19
7YX.7:
16 residues within 4Å:
Chain A:
D.17
,
Y.19
Chain B:
Y.189
,
H.192
,
F.194
,
R.197
,
D.220
,
S.242
,
V.243
,
A.245
,
S.276
,
I.310
,
R.312
,
I.352
,
A.380
Ligands:
EDO.4
13
PLIP interactions
:
12 interactions with chain B
,
1 interactions with chain A
Hydrophobic interactions:
B:Y.189
,
B:D.220
,
B:V.243
,
B:V.243
,
B:I.310
,
B:I.352
,
B:A.380
Hydrogen bonds:
B:S.276
Water bridges:
B:D.220
,
B:S.242
,
B:R.312
pi-Stacking:
B:F.194
,
A:Y.19
1 x
EDO
:
1,2-ETHANEDIOL
(Non-functional Binders)
EDO.4:
7 residues within 4Å:
Chain A:
Y.19
,
K.401
Chain B:
R.197
,
E.247
,
H.248
,
R.312
Ligands:
7YX.7
7
PLIP interactions
:
1 interactions with chain A
,
6 interactions with chain B
Water bridges:
A:F.400
,
B:R.197
,
B:R.197
,
B:R.197
Hydrogen bonds:
B:H.248
,
B:R.312
,
B:R.312
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Bohnke, N. et al., A Novel NAMPT Inhibitor-Based Antibody-Drug Conjugate Payload Class for Cancer Therapy. Bioconjug.Chem. (2022)
Release Date
2022-06-15
Peptides
Nicotinamide phosphoribosyltransferase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
C
B
D
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Nicotinamide phosphoribosyltransferase
Toggle Identical (AB)
Related Entries With Identical Sequence
7ppe.1
|
7ppf.1
|
7ppg.1
|
7pph.1
|
7ppi.1
|
7ppi.2
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