Structure of PDB 5vxa Chain A Binding Site BS02

Receptor Information
>5vxa Chain A (length=178) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSEAAQLLEAADFAARKHRQQRRKDPEGTPYINHPIGVARILTHEAGITD
IVVLQAALLHDTVEKTDTTLDEVELHFGAQVRRLVEEVTDDKTLPKLERK
RLQVEQAPHSSPGAKLVKLADKLYNLRDLNRCTPEGWSEHRVQEYFEWAA
QVVKGLQGTNRQLEEALKHLFKQRGLTI
Ligand information
Ligand IDNDP
InChIInChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyACFIXJIJDZMPPO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
FormulaC21 H30 N7 O17 P3
NameNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ChEMBLCHEMBL407009
DrugBankDB02338
ZINCZINC000008215411
PDB chain5vxa Chain A Residue 202 [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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PDB5vxa MESH1 is a cytosolic NADPH phosphatase that regulates ferroptosis.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		R24 K25 Y32 H35 K66 K97 L98 K101 N126 D129 L130 W138 H141 R142 E145 Y146
Binding residue
(residue number reindexed from 1)		R23 K24 Y31 H34 K65 K96 L97 K100 N125 D128 L129 W137 H140 R141 E144 Y145
Annotation score2
Enzymatic activity
Enzyme Commision number 3.1.7.2: guanosine-3',5'-bis(diphosphate) 3'-diphosphatase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008893 guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:5vxa, PDBe:5vxa, PDBj:5vxa
PDBsum5vxa
PubMed32462112
UniProtQ8N4P3|MESH1_HUMAN Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1 (Gene Name=HDDC3)

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