Structure of PDB 4h2b Chain A Binding Site BS03

Receptor Information

>4h2b Chain A (length=524) Species: 9606 (Homo sapiens)

PWELTILHTNDVHSRLEQTSEDSSKCVDASRCMGGVARLFTKVQQIRRAE
PNVLLLDAGDQYQGTIWFTVYKGAEVAHFMNALRYDAMALGNHEFDNGVE
GLIEPLLKEAKFPILSANISASGPLASQISGLYLPYKVLPVGDEVVGIVG
YTSKETPFLSNPGTNLVFEDEITALQPEVDKLKTLNVNKIIALGHSGFEM
DKLIAQKVRGVDVVVGGHSNTFLYTGNPPSKEVPAGKYPFIVTSDDGRKV
PVVQAYAFGKYLGYLKIEFDERGNVISSHGNPILLDSSIPEDPSIKADIN
KWRIKLDDYSTQELGKTIVYLDGSSQSCRFRECNMGNLICDAMINNNLRH
ADEMFWNHVSMCILNGGGIRSPIDERNDGTITWENLAAVLPFGGTFDLVQ
LKGSTLKKAFEHSVHRYGQSTGEFLQVGGIHVVYDLSRKPGDRVVKLDVL
CTSCRVPSYDPLKMDEVYKVILPNFLANGGDGFQMIKDELLRHDSGDQDI
NVVSTYISKMKVIYPAVEGRIKFS

Ligand information

• Ligand ID: 0XE
• InChI: InChI=1S/C21H18O11/c22-9-6-10(8-4-2-1-3-5-8)30-11-7-12(14(23)15(24)13(9)11)31-21-18(27)16(25)17(26)19(32-21)20(28)29/h1-7,16-19,21,23-27H,(H,28,29)/t16-,17-,18+,19-,21+/m0/s1
• InChIKey: IKIIZLYTISPENI-ZFORQUDYSA-N
• SMILES:
  CACTVS 3.370: O[CH]1[CH](O)[CH](O[CH]([CH]1O)C(O)=O)Oc2cc3OC(=CC(=O)c3c(O)c2O)c4ccccc4
  ACDLabs 12.01: O=C(O)C4OC(Oc3c(O)c(O)c2c(OC(c1ccccc1)=CC2=O)c3)C(O)C(O)C4O
  OpenEye OEToolkits 1.7.6: c1ccc(cc1)C2=CC(=O)c3c(cc(c(c3O)O)O[C@H]4[C@@H]([C@H]([C@@H]([C@H](O4)C(=O)O)O)O)O)O2
  CACTVS 3.370: O[C@@H]1[C@@H](O)[C@@H](O[C@@H]([C@H]1O)C(O)=O)Oc2cc3OC(=CC(=O)c3c(O)c2O)c4ccccc4
  OpenEye OEToolkits 1.7.6: c1ccc(cc1)C2=CC(=O)c3c(cc(c(c3O)O)OC4C(C(C(C(O4)C(=O)O)O)O)O)O2
• Formula: C21 H18 O11
• Name: 5,6-dihydroxy-4-oxo-2-phenyl-4H-chromen-7-yl beta-D-glucopyranosiduronic acid;
  Baicalin
• ChEMBL: CHEMBL485818
• ZINC: ZINC000003943903
• PDB chain: 4h2b Chain A Residue 603

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4h2b Crystal Structure of the Human Ecto-5'-Nucleotidase (CD73): Insights into the Regulation of Purinergic Signaling.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): D47 R354 N390 G392 G393 R395 F417 G447 F500 D506
• Binding residue (residue number reindexed from 1): D22 R329 N365 G367 G368 R370 F392 G422 F475 D481
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D36 H38 D85 N117 H118 D121 H220 H243 N245 S350 R354 R395
• Catalytic site (residue number reindexed from 1): D11 H13 D60 N92 H93 D96 H195 H218 N220 S325 R329 R370
• Enzyme Commision number: 3.1.3.35: thymidylate 5'-phosphatase.
  3.1.3.5: 5'-nucleotidase.
  3.1.3.89: 5'-deoxynucleotidase.
  3.1.3.91: 7-methylguanosine nucleotidase.
  3.1.3.99: IMP-specific 5'-nucleotidase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0002953 5'-deoxynucleotidase activity
• GO:0005515 protein binding
• GO:0008252 nucleotidase activity
• GO:0008253 5'-nucleotidase activity
• GO:0008270 zinc ion binding
• GO:0016787 hydrolase activity
• GO:0016788 hydrolase activity, acting on ester bonds
• GO:0042802 identical protein binding
• GO:0046872 metal ion binding
• GO:0050340 thymidylate 5'-phosphatase activity
• GO:0050483 IMP 5'-nucleotidase activity
• GO:0050484 GMP 5'-nucleotidase activity
• GO:0106411 XMP 5'-nucleosidase activity

Biological Process

• GO:0006196 AMP catabolic process
• GO:0006259 DNA metabolic process
• GO:0007159 leukocyte cell-cell adhesion
• GO:0009166 nucleotide catabolic process
• GO:0033198 response to ATP
• GO:0046032 ADP catabolic process
• GO:0046034 ATP metabolic process
• GO:0046086 adenosine biosynthetic process
• GO:0050728 negative regulation of inflammatory response
• GO:0055074 calcium ion homeostasis
• GO:0140928 inhibition of non-skeletal tissue mineralization

Cellular Component

• GO:0005654 nucleoplasm
• GO:0005829 cytosol
• GO:0005886 plasma membrane
• GO:0009897 external side of plasma membrane
• GO:0009986 cell surface
• GO:0016020 membrane
• GO:0070062 extracellular exosome
• GO:0098552 side of membrane

External links

• PDB: RCSB:4h2b, PDBe:4h2b, PDBj:4h2b
• PDBsum: 4h2b
• PubMed: 23142347
• UniProt: P21589|5NTD_HUMAN 5'-nucleotidase (Gene Name=NT5E)