Structure of PDB 5gvn Chain A Binding Site BS01

Receptor Information

>5gvn Chain A (length=442) Species: 126793 (Plasmodium vivax Sal-1)

MFNNEPLEQIDKELHDILADEEKRQRETINLIASENLTNGAVRECLGNRV
SNKYSEGYPKKRYYGGNDFIDKIEELCQKRALEAFNVSDEEWGVNVQPLS
GSAANVQALYALVGVKGKIMGMHLCSGGHLTHGFFDEKKKVSITSDMFES
KLYKCNSQGYVDLDAVREMALSFKPKVIICGYTSYPRDIDYQQFRQICDE
VNAYLFADISHISSFVACNILNNPFLHADVVTTTTHKILRGPRSALIFFN
KKRNPGIEQKINSAVFPSFQGGPHNNKIAAVACQLKEVHSPAFKEYTQQV
LLNSKALAKALISKQIDLVTNGTDNHLIVVDLRKFSITGSKLQETCNAIN
VSLNKNTIPSDVDCVSPSGVRIGTPAMTTRGAKEKDMEFIADVLARAIKI
TVDLQEQYGKKLVDFKKGLPGNAQLQQLKQEVVTWAGALPFP

Ligand information

• Ligand ID: PLG
• InChI: InChI=1S/C10H15N2O7P/c1-6-10(15)8(3-11-4-9(13)14)7(2-12-6)5-19-20(16,17)18/h2,11,15H,3-5H2,1H3,(H,13,14)(H2,16,17,18)
• InChIKey: FEVQWBMNLWUBTF-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: Cc1ncc(CO[P](O)(O)=O)c(CNCC(O)=O)c1O
  ACDLabs 10.04: O=P(O)(O)OCc1cnc(c(O)c1CNCC(=O)O)C
  OpenEye OEToolkits 1.5.0: Cc1c(c(c(cn1)COP(=O)(O)O)CNCC(=O)O)O
• Formula: C10 H15 N2 O7 P
• Name: N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE];
  N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE
• DrugBank: DB02824
• ZINC: ZINC000002046831
• PDB chain: 5gvn Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5gvn Antimalarial Inhibitors Targeting Serine Hydroxymethyltransferase (SHMT) with in Vivo Efficacy and Analysis of their Binding Mode Based on X-ray Cocrystal Structures
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): S34 S100 G101 S102 H129 Y182 T183 D208 H211 H236 K237 R371
• Binding residue (residue number reindexed from 1): S34 S100 G101 S102 H129 Y182 T183 D208 H211 H236 K237 R371
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): Y54 E56 D208 T234 K237 R243
• Catalytic site (residue number reindexed from 1): Y54 E56 D208 T234 K237 R243
• Enzyme Commision number: 2.1.2.1: glycine hydroxymethyltransferase.

Gene Ontology

Molecular Function

• GO:0004372 glycine hydroxymethyltransferase activity
• GO:0008270 zinc ion binding
• GO:0016740 transferase activity
• GO:0030170 pyridoxal phosphate binding
• GO:0050897 cobalt ion binding
• GO:0070905 serine binding

Biological Process

• GO:0006565 L-serine catabolic process
• GO:0006730 one-carbon metabolic process
• GO:0019264 glycine biosynthetic process from serine
• GO:0035999 tetrahydrofolate interconversion
• GO:0046653 tetrahydrofolate metabolic process
• GO:0046655 folic acid metabolic process

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:5gvn, PDBe:5gvn, PDBj:5gvn
• PDBsum: 5gvn
• PubMed: 28537728
• UniProt: A5K8L9