Structure of PDB 3gzn Chain B Binding Site BS02

Receptor Information
>3gzn Chain B (length=429) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DWEGRWNHVKKFLERSGPFTHPDFEPSTESLQFLLDTCKVLVIGAGGLGC
ELLKNLALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKAEVAAEFL
NDRVPNCNVVPHFNKIQDFNDTFYRQFHIIVCGLDSIIARRWINGMLISL
LNYEDGVLDPSSIVPLIDGGTEGFKGNARVILPGMTACIECTLELYPPQV
NFPMCTIASMPRLPEHCIEYVRMLQWPKEQPFGEGVPLDGDDPEHIQWIF
QKSLERASQYNIRGVTYRLTQGVVKRIIPAVASTNAVIAAVCATEVFKIA
TSAYIPLNNYLVFNDVDGLYTYTFEAERKENCPACSQLPQNIQFSPSAKL
QEVLDYLTNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKL
KELGLVDGQELAVADVTTPQTVLFKLHFT
Ligand information
Ligand IDB39
InChIInChI=1S/C21H25N5O4S/c22-31(28,29)30-11-14-9-15(10-19(14)27)26-8-7-17-20(23-12-24-21(17)26)25-18-6-5-13-3-1-2-4-16(13)18/h1-4,7-8,12,14-15,18-19,27H,5-6,9-11H2,(H2,22,28,29)(H,23,24,25)/t14-,15+,18-,19-/m0/s1
InChIKeyMPUQHZXIXSTTDU-QXGSTGNESA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[S](=O)(=O)OC[C@@H]1C[C@H](C[C@@H]1O)n2ccc3c(N[C@H]4CCc5ccccc45)ncnc23
OpenEye OEToolkits 1.5.0c1ccc2c(c1)CCC2Nc3c4ccn(c4ncn3)C5CC(C(C5)O)COS(=O)(=O)N
ACDLabs 10.04O=S(=O)(OCC5CC(n2c1ncnc(c1cc2)NC4c3ccccc3CC4)CC5O)N
CACTVS 3.341N[S](=O)(=O)OC[CH]1C[CH](C[CH]1O)n2ccc3c(N[CH]4CCc5ccccc45)ncnc23
OpenEye OEToolkits 1.5.0c1ccc2c(c1)CC[C@@H]2Nc3c4ccn(c4ncn3)[C@@H]5C[C@H]([C@H](C5)O)COS(=O)(=O)N
FormulaC21 H25 N5 O4 S
Name[(1S,2S,4R)-4-{4-[(1S)-2,3-dihydro-1H-inden-1-ylamino]-7H-pyrrolo[2,3-d]pyrimidin-7-yl}-2-hydroxycyclopentyl]methyl sulfamate
ChEMBLCHEMBL1231160
DrugBankDB11759
ZINCZINC000058660702
PDB chain3gzn Chain I Residue 464 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3gzn Substrate-assisted inhibition of ubiquitin-like protein-activating enzymes: the NEDD8 E1 inhibitor MLN4924 forms a NEDD8-AMP mimetic in situ.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		G78 G79 D100 M101 D102 K147 I148 Q149 L166 D167 A171 W174
Binding residue
(residue number reindexed from 1)		G46 G47 D68 M69 D70 K115 I116 Q117 L134 D135 A139 W142
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.00,IC50=10nM
BindingDB: IC50=5.0nM
Enzymatic activity
Catalytic site (original residue number in PDB) K42 D167 C237 T238 A240
Catalytic site (residue number reindexed from 1) K10 D135 C205 T206 A208
Enzyme Commision number 6.2.1.64: E1 NEDD8-activating enzyme.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008641 ubiquitin-like modifier activating enzyme activity
GO:0016874 ligase activity
GO:0019781 NEDD8 activating enzyme activity
GO:0019788 NEDD8 transferase activity
GO:0042802 identical protein binding
GO:0046982 protein heterodimerization activity
Biological Process
GO:0000278 mitotic cell cycle
GO:0006508 proteolysis
GO:0007113 endomitotic cell cycle
GO:0036211 protein modification process
GO:0043687 post-translational protein modification
GO:0045116 protein neddylation
GO:0051726 regulation of cell cycle
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0032991 protein-containing complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3gzn, PDBe:3gzn, PDBj:3gzn
PDBsum3gzn
PubMed20129059
UniProtQ8TBC4|UBA3_HUMAN NEDD8-activating enzyme E1 catalytic subunit (Gene Name=UBA3)

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