Structure of PDB 8cd0 Chain A Binding Site BS01

Receptor Information
>8cd0 Chain A (length=716) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PLVLVFVESLYSQLGQEVVAILESSRFKYRTEIAPTLTDKGRGRFALIIY
ENILKYVNLDAWNRELLDKYCVAYGVGIIGFFDCSINPKSPLLYVTRPSE
VFQSNHSTYEPVLLATVVQDLGLHDGIQRVLFGNNLNFWLHKLVFVDAVA
FLTGKRLSLPLDRYILVDIDDIFVGKEGTRMKVEDVKALFDTQNELRAHI
PNFTFNLGYSGKFFHTGTNAEDAGDDLLLSYVKEFWWFPHMWSHMQPHLF
HNQSVLAEQMALNKKFAVEHGIPTDMGYAVAPHHSGVYPVHVQLYEAWKQ
VWSIRVTSTEEYPHLKPARYRRGFIHNGIMVLPRQTCGLFTHTIFYNEYP
GGSSELDKIINGGELFLTVLLNPISIFMTHLSNYGNDRLGLYTFKHLVRF
LHSWTNLRLQTLPPVQLAQKYFQIFSEEKDPLWQDPCEDKRHKDIWSKEK
TCDRFPKLLIIGPQKTGTTALYLFLGMHPDLSSNYPSSETFEEIQFFNGH
NYHKGIDWYMEFFPIPSNTTSDFYFEKSANYFDSEVAPRRAAALLPKAKV
LTILINPADRAYSWYQHQRAHDDPVALKYTFHEVISSKLRALQNRCLVPG
WYATHIERWLSAYHANQILVLDGKLLRTEPAKVMDMVQKFLGVTNTIDYH
KTLAFDPKKGFWCCLGKSKGRKYPEMDLDSRAFLKDYYRDHNIELSKLLY
KMGQTLPTWLREDLQN
Ligand information
Ligand IDA3P
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-6(16)7(25-27(20,21)22)4(24-10)1-23-26(17,18)19/h2-4,6-7,10,16H,1H2,(H2,11,12,13)(H2,17,18,19)(H2,20,21,22)/t4-,6-,7-,10-/m1/s1
InChIKeyWHTCPDAXWFLDIH-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)OP(=O)(O)O)O)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)OP(=O)(O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O[P](O)(O)=O)[C@H]3O
ACDLabs 10.04O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O
FormulaC10 H15 N5 O10 P2
NameADENOSINE-3'-5'-DIPHOSPHATE
ChEMBLCHEMBL574817
DrugBankDB01812
ZINCZINC000004228234
PDB chain8cd0 Chain A Residue 901 [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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PDB8cd0 Structural and mechanistic characterization of bifunctional heparan sulfate N-deacetylase-N-sulfotransferase 1
Resolution2.42 Å
Binding residue
(original residue number in PDB)		K614 T615 G616 T617 T618 A619 L781 R782 F816 K833
Binding residue
(residue number reindexed from 1)		K465 T466 G467 T468 T469 A470 L626 R627 F661 K669
Annotation score5
Enzymatic activity
Enzyme Commision number 2.8.2.8: [heparan sulfate]-glucosamine N-sulfotransferase.
3.5.1.-
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008146 sulfotransferase activity
GO:0015016 [heparan sulfate]-glucosamine N-sulfotransferase activity
GO:0016740 transferase activity
GO:0016787 hydrolase activity
GO:0019213 deacetylase activity
GO:0050119 N-acetylglucosamine deacetylase activity
GO:0102140 heparan sulfate N-deacetylase activity
Biological Process
GO:0000271 polysaccharide biosynthetic process
GO:0003279 cardiac septum development
GO:0006954 inflammatory response
GO:0007507 heart development
GO:0007585 respiratory gaseous exchange by respiratory system
GO:0008283 cell population proliferation
GO:0008543 fibroblast growth factor receptor signaling pathway
GO:0009887 animal organ morphogenesis
GO:0015012 heparan sulfate proteoglycan biosynthetic process
GO:0015014 heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process
GO:0015015 heparan sulfate proteoglycan biosynthetic process, enzymatic modification
GO:0030203 glycosaminoglycan metabolic process
GO:0030210 heparin biosynthetic process
GO:0030900 forebrain development
GO:0030901 midbrain development
GO:0035904 aorta development
GO:0043410 positive regulation of MAPK cascade
GO:0045880 positive regulation of smoothened signaling pathway
GO:0048702 embryonic neurocranium morphogenesis
GO:0048703 embryonic viscerocranium morphogenesis
GO:0060976 coronary vasculature development
Cellular Component
GO:0000139 Golgi membrane
GO:0005794 Golgi apparatus
GO:0016020 membrane
GO:0032588 trans-Golgi network membrane

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8cd0, PDBe:8cd0, PDBj:8cd0
PDBsum8cd0
PubMed38351061
UniProtP52848|NDST1_HUMAN Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1 (Gene Name=NDST1)

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