Structure of PDB 1njj Chain D Binding Site BS02

Receptor Information
>1njj Chain D (length=354) Species: 31285 (Trypanosoma brucei gambiense) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NTRDALCKKISGDPFFVADLGDIVRKHETWKKCLPRVTPFYAVKCNDDWR
VLGTLAALGTGFDCASNTEIQRVRGIGVPPEKIIYANPCKQISHIRYARD
SGVDVMTFDCVDELEKVAKTHPKAKMVLRISTVKFGAKVEDCRFILEQAK
KLNIDVTGVSFHVGSGSTDASTFAQAISDSRFVFDMGTELGFNMHILDIG
GGFPGTRDAPLKFEEIAGVINNALEKHFPPDLKLTIVAEPGRYYVASAFT
LAVNVIAKKVTSNAQSFMYYVNDGVYGSFNCILYDHAVVRPLPQREPIPN
EKLYPSSVWGPTCDGLDQIVERYYLPEMQVGEWLLFEDMGAYTVFQSPTI
YYVV
Ligand information
Ligand IDORX
InChIInChI=1S/C13H22N3O7P/c1-8-12(17)10(6-16-11(13(18)19)3-2-4-14)9(5-15-8)7-23-24(20,21)22/h5,11,16-17H,2-4,6-7,14H2,1H3,(H,18,19)(H2,20,21,22)/t11-/m1/s1
InChIKeyOIRLUPUXIUAWOH-LLVKDONJSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)C(NCc1c(cnc(c1O)C)COP(=O)(O)O)CCCN
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(CN[C@H](CCCN)C(O)=O)c1O
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(CN[CH](CCCN)C(O)=O)c1O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@H](CCCN)C(=O)O)O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CNC(CCCN)C(=O)O)O
FormulaC13 H22 N3 O7 P
NameN~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-ORNITHINE
ChEMBL
DrugBank
ZINCZINC000002047626
PDB chain1njj Chain D Residue 426 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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)		K69 H197 G237 E274 G276 R277 Y331 D332 Y389
Binding residue
(residue number reindexed from 1)		K44 H162 G202 E239 G241 R242 Y284 D285 Y342
Annotation score1
Binding affinityMOAD: Kd=0.27mM
Enzymatic activity
Catalytic site (original residue number in PDB) K69 H197 E274
Catalytic site (residue number reindexed from 1) K44 H162 E239
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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