Structure of PDB 9box Chain D Binding Site BS04

Receptor Information
>9box Chain D (length=453) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
WTGQESLSDSDPEMWELLQREKDRQCRGLELIASENFCSRAALEALGSCL
NNKYSEGYPGKRYYGGAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPYS
GSPANLAVYTALLQPHDRIMGLDLPDGGHLTHGYMSDVKRISATSIFFES
MPYKLNPKTGLIDYNQLALTARLFRPRLIIAGTSAYARLIDYARMREVCD
EVKAHLLADMAHISGLVAAKVIPSPFKHADIVTTTTHKTLRGARSGLIFY
RKGVKAPYTFEDRINFAVFPSLQGGPHNHAIAAVAVALKQACTPMFREYS
LQVLKNARAMADALLERGYSLVSGGTDNHLVLVDLRPKGLDGARAERVLE
LVSITANKNTCPGDRSAITPGGLRLGAPALTSRQFREDDFRRVVDFIDEG
VNIGLEVKSKTAKLQDFKSFLLKDSETSQRLANLRQRVEQFARAFPMPGF
DEH
Ligand information
Ligand IDFFO
InChIInChI=1S/C20H23N7O7/c21-20-25-16-15(18(32)26-20)27(9-28)12(8-23-16)7-22-11-3-1-10(2-4-11)17(31)24-13(19(33)34)5-6-14(29)30/h1-4,9,12-13,22H,5-8H2,(H,24,31)(H,29,30)(H,33,34)(H4,21,23,25,26,32)/t12-,13-/m0/s1
InChIKeyVVIAGPKUTFNRDU-STQMWFEESA-N
SMILES
SoftwareSMILES
CACTVS 3.370NC1=NC2=C(N(C=O)[CH](CNc3ccc(cc3)C(=O)N[CH](CCC(O)=O)C(O)=O)CN2)C(=O)N1
OpenEye OEToolkits 1.7.2c1cc(ccc1C(=O)NC(CCC(=O)O)C(=O)O)NCC2CNC3=C(N2C=O)C(=O)NC(=N3)N
ACDLabs 12.01O=C(O)C(NC(=O)c1ccc(cc1)NCC2N(C=O)C=3C(=O)NC(=NC=3NC2)N)CCC(=O)O
CACTVS 3.370NC1=NC2=C(N(C=O)[C@@H](CNc3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)CN2)C(=O)N1
FormulaC20 H23 N7 O7
NameN-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid;
[6S]-5-FORMYL-TETRAHYDROFOLATE;
6S-FOLINIC ACID
ChEMBLCHEMBL1908841
DrugBankDB11596
ZINCZINC000009212427
PDB chain9box Chain D Residue 602 [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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PDB9box Universality of critical active site glutamate as an acid-base catalyst in serine hydroxymethyltransferase function.
Resolution2.1 Å
Binding residue
(original residue number in PDB)
L166 G169 G170 H171 S226 N410 S417 A418 I419
Binding residue
(residue number reindexed from 1)
L124 G127 G128 H129 S184 N359 S366 A367 I368
Annotation score3
External links
PDB RCSB:9box, PDBe:9box, PDBj:9box
PDBsum9box
PubMed39148791
UniProtP34897|GLYM_HUMAN Serine hydroxymethyltransferase, mitochondrial (Gene Name=SHMT2)

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