Structure of PDB 3kyd Chain B Binding Site BS02

Receptor Information
>3kyd Chain B (length=477) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SRGLPRELAEAVAGGRVLVVGAGGIGCELLKNLVLTGFSHIDLIDLDTID
VSNLNRQFLFQKKHVGRSKAQVAKESVLQFYPKANIVAYHDSIMNPDYNV
EFFRQFILVMNALDNRAARNHVNRMCLAADVPLIESGTAGYLGQVTTIKK
GVTECYECHPKPTQRTFPGCTIRNTPSEPIHCIVWAKYLFNQLFTKEWAK
STGYDPVKLFTKLFKDDIRYLLTMDKLWRKRKPPVPLDWAEVQSQDQQVL
DVKSYARLFSKSIETLRVHLAEKDKDDPSAMDFVTSAANLRMHIFSMNMK
SRFDIKSMAGNIIPAIATTNAVIAGLIVLEGLKILSGKIDQCRTIFLNKQ
PNPRKKLLVPCALDPPNPNCYVCASKPEVTVRLNVHKVTVLTLQDKIVKE
KFAMVAPDVQIEDGKGTILISSEEGETEANNHKKLSEFGIRNGSRLQADD
FLQDYTLLINILHSEDLGKDVEFEVVG
Ligand information
Ligand IDVMX
InChIInChI=1S/C13H21N7O5S/c14-2-1-3-26(23,24)19-4-7-9(21)10(22)13(25-7)20-6-18-8-11(15)16-5-17-12(8)20/h5-7,9-10,13,19,21-22H,1-4,14H2,(H2,15,16,17)/t7-,9-,10-,13-/m1/s1
InChIKeyGCNSCCULRVBOML-QYVSTXNMSA-N
SMILES
SoftwareSMILES
CACTVS 3.352NCCC[S](=O)(=O)NC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.352NCCC[S](=O)(=O)NC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CNS(=O)(=O)CCCN)O)O)N
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CNS(=O)(=O)CCCN)O)O)N
FormulaC13 H21 N7 O5 S
Name5'-{[(3-aminopropyl)sulfonyl]amino}-5'-deoxyadenosine
ChEMBL
DrugBank
ZINCZINC000058638696
PDB chain3kyd Chain D Residue 97 [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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PDB3kyd Active site remodelling accompanies thioester bond formation in the SUMO E1.
Resolution2.61 Å
Binding residue
(original residue number in PDB)		I28 D48 L49 K72 S95 I96 L116 D117 N118 C173 R176
Binding residue
(residue number reindexed from 1)		I25 D45 L46 K69 S92 I93 L113 D114 N115 C170 R173
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D117 C173 T174 R176
Catalytic site (residue number reindexed from 1) D114 C170 T171 R173
Enzyme Commision number 2.3.2.-
Gene Ontology
Molecular Function
GO:0008641 ubiquitin-like modifier activating enzyme activity
GO:0019948 SUMO activating enzyme activity
Biological Process
GO:0016925 protein sumoylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3kyd, PDBe:3kyd, PDBj:3kyd
PDBsum3kyd
PubMed20164921
UniProtQ9UBT2|SAE2_HUMAN SUMO-activating enzyme subunit 2 (Gene Name=UBA2)

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