Structure of PDB 5gvp Chain C Binding Site BS01

Receptor Information

>5gvp Chain C (length=442) Species: 126793 (Plasmodium vivax Sal-1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

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

Software	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

PDB chain

5gvp Chain C Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	5gvp Antimalarial Inhibitors Targeting Serine Hydroxymethyltransferase (SHMT) with in Vivo Efficacy and Analysis of their Binding Mode Based on X-ray Cocrystal Structures
Resolution	2.26 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

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External links

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

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