Structure of PDB 1p4m Chain A Binding Site BS01

Receptor Information
>1p4m Chain A (length=147) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RHLPYFCRGQVVRGFGRGSKQLGIPTANFPEQVVDNLPADISTGIYYGWA
SVGSGDVHKMVVSIGWNPYYKNTKKSMETHIMHTFKEDFYGEILNVAIVG
YLRPEKNFDSLESLISAIQGDIEEAKKRLELPEYLKIKEDNFFQVSK
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-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)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain1p4m Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1p4m Crystal Structure of Human Riboflavin Kinase Reveals a Beta Barrel Fold and a Novel Active Site Arch
Resolution1.8 Å
Binding residue
(original residue number in PDB)		G22 G26 S27 K28 P33 T34 N36 I89 F93 D96 F97 Y98
Binding residue
(residue number reindexed from 1)		G14 G18 S19 K20 P25 T26 N28 I81 F85 D88 F89 Y90
Annotation score5
Enzymatic activity
Enzyme Commision number 2.7.1.26: riboflavin kinase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008531 riboflavin kinase activity
GO:0016301 kinase activity
GO:0046872 metal ion binding
Biological Process
GO:0006771 riboflavin metabolic process
GO:0006915 apoptotic process
GO:0009231 riboflavin biosynthetic process
GO:0009398 FMN biosynthetic process
GO:0016310 phosphorylation
GO:0033864 positive regulation of NAD(P)H oxidase activity
GO:0072388 flavin adenine dinucleotide biosynthetic process
GO:0072593 reactive oxygen species metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1p4m, PDBe:1p4m, PDBj:1p4m
PDBsum1p4m
PubMed12623014
UniProtQ969G6|RIFK_HUMAN Riboflavin kinase (Gene Name=RFK)

[Back to BioLiP]