Target Binding Site Detail

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Target General Information
Ligand General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T93995 Target Info
Target Name Ubiquitin-like protein Nedd8 (NEDD8)
Synonyms Neural precursor cell expressed developmentally down-regulated protein 8; Neddylin; NEDD-8
Target Type Clinical trial Target
Gene Name NEDD8
Biochemical Class Ubiquitin family
UniProt ID
NEDD8_HUMAN
Ligand General Information  Top
Ligand Name Adenosine triphosphate Ligand Info
Canonical SMILES C1=NC(=C2C(=N1)N(C=N2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
InChI 1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKey ZKHQWZAMYRWXGA-KQYNXXCUSA-N
PubChem Compound ID 5957
Drug Binding Sites of Target  Top
PDB ID: 2NVU      Structure of APPBP1-UBA3~NEDD8-NEDD8-MgATP-Ubc12(C111A), a trapped ubiquitin-like protein activation complex
Method X-ray diffraction Resolution 2.80 Å Mutation Yes [1]
PDB Sequence
MLIKVKTLTG
10
KEIEIDIEPT
20
DKVERIKERV
30
EEKEGIPPQQ
40
QRLIYSGKQM
50

NDEKTAADYK
60
ILGGSVLHLV
70
LALRGG
Residue
Distance (Å)
GLY75
4.968
Residue
Distance (Å)
GLY76
2.896
PDB ID: 1R4N      APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex with ATP
Method X-ray diffraction Resolution 3.60 Å Mutation Yes [2]
PDB Sequence
MLIKVKTLTG
110
KEIEIDIEPT
120
DKVERIKERV
130
EEKEGIPPQQ
140
QRLIYSGKQM
150

NDEKTAADYK
160
ILGGSVLHLV
170
LALRGG
Residue
Distance (Å)
GLY176
2.788
Residue
Distance (Å)
References  Top
REF 1 Basis for a ubiquitin-like protein thioester switch toggling E1-E2 affinity. Nature. 2007 Jan 25;445(7126):394-8.
REF 2 The structure of the APPBP1-UBA3-NEDD8-ATP complex reveals the basis for selective ubiquitin-like protein activation by an E1. Mol Cell. 2003 Dec;12(6):1427-37.

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