Structure of PDB 4pab Chain B Binding Site BS02

Receptor Information
>4pab Chain B (length=824) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EWKDRAETVIIGGGCVGVSLAYHLAKAGMRDVVLLEKSELTAGSTWHAAG
LTTYFHPGINLKKIHYDSIKLYERLEEETGQVVGFHQPGSIRLATTPERV
DEFKYQMTRTNWHATEQYIIEPEKIHELFPLLNMDKILAGLYNPGDGHID
PYSLTMALATGARKYGVLLKYPAPVTSLKPRPDGTWDVETPQGSVRANRI
VNAAGFWAREVGKMIGLDHPLIPVQHQYVVTSTIPEVKALKRELPVLRDL
EGSYYLRQERDGLLFGPYESQEKMKLQASWVAHGVPPGFGKELFESDLDR
ITEHVEAAMEMVPVLKKADIINIVNGPITYSPDILPMVGPHQGVRNYWVA
IGFGYGIIHAGGVGKYLSDWILHGEPPFDLIELDPNRYGKWTTTQYTEAK
ARESYGFNNIVGYPKEERFAGRPTQRVSGLYKILESKCSMGFHAGWEQPH
WFYKPGQDTQYRPSFRRTNWFRPVGSEYKQVMQRVGVIDLSPFGKFNIKG
QDSTQLLDHLCANVIPKVGFTNISHMLTPRGRVYAELTVSHQSPGEFLLI
TGSGSELHDLRWIEEAAVRGGYDVEIRNITDELGVLGVAGPYARRVLQKL
TSEDLSDDVFKFLQTKSLKISDIPVTAIRISYTGELGWELYHRREDSAAL
YERIMNAGQEEGIDNFGTYALNALRLEKAFRAWGSEMNCDTNPLEAGLDY
FIKLNKPADFTGKQALKQIKAKGLKRRLVCLTLATDDVDPEGNESVWYKG
KVIGNTTSGSYSYSIQKSLAFAYVPVELSEVGQQVEVELLGKNYPATIIQ
EPLVLTEPTRTRLQKDGRKSAALE
Ligand information
Ligand IDTHG
InChIInChI=1S/C19H23N7O6/c20-19-25-15-14(17(30)26-19)23-11(8-22-15)7-21-10-3-1-9(2-4-10)16(29)24-12(18(31)32)5-6-13(27)28/h1-4,11-12,21,23H,5-8H2,(H,24,29)(H,27,28)(H,31,32)(H4,20,22,25,26,30)/t11-,12-/m0/s1
InChIKeyMSTNYGQPCMXVAQ-RYUDHWBXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NC[C@H]2CNC3=C(N2)C(=O)NC(=N3)N
CACTVS 3.341NC1=NC2=C(N[CH](CNc3ccc(cc3)C(=O)N[CH](CCC(O)=O)C(O)=O)CN2)C(=O)N1
OpenEye OEToolkits 1.5.0c1cc(ccc1C(=O)NC(CCC(=O)O)C(=O)O)NCC2CNC3=C(N2)C(=O)NC(=N3)N
ACDLabs 10.04O=C(O)C(NC(=O)c1ccc(cc1)NCC3NC=2C(=O)NC(=NC=2NC3)N)CCC(=O)O
CACTVS 3.341NC1=NC2=C(N[C@@H](CNc3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)CN2)C(=O)N1
FormulaC19 H23 N7 O6
Name(6S)-5,6,7,8-TETRAHYDROFOLATE
ChEMBL
DrugBankDB02031
ZINCZINC000004228237
PDB chain4pab Chain B Residue 902 [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]
PDB4pab Folate in demethylation: The crystal structure of the rat dimethylglycine dehydrogenase complexed with tetrahydrofolate.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		I560 E573 T575 I587 F649 L650 Y669 E676 F717 Y737
Binding residue
(residue number reindexed from 1)		I523 E536 T538 I550 F612 L613 Y632 E639 F680 Y700
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) T90 E139 H263 Y292 E573
Catalytic site (residue number reindexed from 1) T53 E102 H226 Y255 E536
Enzyme Commision number 1.5.8.4: dimethylglycine dehydrogenase.
Gene Ontology
Molecular Function
GO:0005542 folic acid binding
GO:0016491 oxidoreductase activity
GO:0047865 dimethylglycine dehydrogenase activity
GO:0050660 flavin adenine dinucleotide binding
Biological Process
GO:0006579 amino-acid betaine catabolic process
GO:0019695 choline metabolic process
GO:0035999 tetrahydrofolate interconversion
GO:0042426 choline catabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4pab, PDBe:4pab, PDBj:4pab
PDBsum4pab
PubMed24858690
UniProtQ63342|M2GD_RAT Dimethylglycine dehydrogenase, mitochondrial (Gene Name=Dmgdh)

[Back to BioLiP]