Structure of PDB 1njj Chain A Binding Site BS01

Receptor Information
>1njj Chain A (length=349) Species: 31285 (Trypanosoma brucei gambiense) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NTRDALCKKGDPFFVADLGDIVRKHETWKKCLPRVTPFYAVKCNDDWRVL
GTLAALGTGFDCASNTEIQRVRGIGVPPEKIIYANPCKQISHIRYARDSG
VDVMTFDCVDELEKVAKTHPKAKMVLRISTVKFGAKVEDCRFILEQAKKL
NIDVTGVSFHVGSGSTDASTFAQAISDSRFVFDMGTELGFNMHILDIGGG
FPGTRDAPLKFEEIAGVINNALEKHFPPDLKLTIVAEPGRYYVASAFTLA
VNVIAKKVTQSFMYYVNDGVYGSFNCILYDHAVVRPLPQREPEKLYPSSV
WGPTCDGLDQIVERYYLPEMQVGEWLLFEDMGAYTVSPTIYYVVSGLPD
Ligand information
Ligand IDGET
InChIInChI=1S/C20H40N4O10/c1-6(25)14-11(27)10(26)9(23)18(32-14)33-15-7(21)4-8(22)16(12(15)28)34-19-13(29)17(24-3)20(2,30)5-31-19/h6-19,24-30H,4-5,21-23H2,1-3H3/t6-,7+,8-,9-,10-,11+,12+,13-,14-,15-,16+,17-,18-,19-,20+/m1/s1
InChIKeyBRZYSWJRSDMWLG-DJWUNRQOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C[C@H]([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@H]2[C@H](C[C@H]([C@@H]([C@H]2O)O[C@@H]3[C@@H]([C@H]([C@@](CO3)(C)O)NC)O)N)N)N)O)O)O
CACTVS 3.341CN[CH]1[CH](O)[CH](OC[C]1(C)O)O[CH]2[CH](N)C[CH](N)[CH](O[CH]3O[CH]([CH](C)O)[CH](O)[CH](O)[CH]3N)[CH]2O
OpenEye OEToolkits 1.5.0CC(C1C(C(C(C(O1)OC2C(CC(C(C2O)OC3C(C(C(CO3)(C)O)NC)O)N)N)N)O)O)O
ACDLabs 10.04O(C2C(O)C(OC1OC(C(O)C)C(O)C(O)C1N)C(N)CC2N)C3OCC(O)(C(NC)C3O)C
CACTVS 3.341CN[C@@H]1[C@@H](O)[C@H](OC[C@]1(C)O)O[C@H]2[C@H](N)C[C@H](N)[C@@H](O[C@H]3O[C@H]([C@@H](C)O)[C@@H](O)[C@H](O)[C@H]3N)[C@@H]2O
FormulaC20 H40 N4 O10
NameGENETICIN;
G418
ChEMBLCHEMBL215226
DrugBankDB04263
ZINCZINC000043543817
PDB chain1njj Chain A Residue 601 [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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PDB1njj X-ray Structure Determination of Trypanosoma brucei Ornithine Decarboxylase Bound to D-Ornithine and to G418: INSIGHTS INTO SUBSTRATE BINDING AND ODC CONFORMATIONAL FLEXIBILITY.
Resolution2.45 Å
Binding residue
(original residue number in PDB)		R22 D243 L339 L382 E384 D385
Binding residue
(residue number reindexed from 1)		R3 D206 L287 L327 E329 D330
Annotation score1
Binding affinityMOAD: Ki=8mM
PDBbind-CN: -logKd/Ki=2.10,Ki=8mM
Enzymatic activity
Catalytic site (original residue number in PDB) K69 H197 E274
Catalytic site (residue number reindexed from 1) K42 H160 E237
Enzyme Commision number 4.1.1.17: ornithine decarboxylase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004586 ornithine decarboxylase activity
GO:0016829 lyase activity
Biological Process
GO:0006596 polyamine biosynthetic process
GO:0033387 putrescine biosynthetic process from ornithine
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1njj, PDBe:1njj, PDBj:1njj
PDBsum1njj
PubMed12672797
UniProtQ9TZZ6

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