Structure of PDB 5gvm Chain A Binding Site BS02

Receptor Information
>5gvm Chain A (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 IDG57
InChIInChI=1S/C26H23F3N4O3/c1-13(2)25(20(12-30)23(31)36-24-22(25)14(3)32-33-24)18-9-17(10-19(11-18)26(27,28)29)16-6-4-5-15(7-16)8-21(34)35/h4-7,9-11,13H,8,31H2,1-3H3,(H,32,33)(H,34,35)/t25-/m0/s1
InChIKeyDBCDVNKPJCGLLK-VWLOTQADSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)[C]1(c2cc(cc(c2)C(F)(F)F)c3cccc(CC(O)=O)c3)C(=C(N)Oc4n[nH]c(C)c14)C#N
CACTVS 3.385CC(C)[C@]1(c2cc(cc(c2)C(F)(F)F)c3cccc(CC(O)=O)c3)C(=C(N)Oc4n[nH]c(C)c14)C#N
OpenEye OEToolkits 2.0.6Cc1c2c(n[nH]1)OC(=C([C@@]2(c3cc(cc(c3)C(F)(F)F)c4cccc(c4)CC(=O)O)C(C)C)C#N)N
OpenEye OEToolkits 2.0.6Cc1c2c(n[nH]1)OC(=C(C2(c3cc(cc(c3)C(F)(F)F)c4cccc(c4)CC(=O)O)C(C)C)C#N)N
FormulaC26 H23 F3 N4 O3
Name2-[3-[3-[(4~{S})-6-azanyl-5-cyano-3-methyl-4-propan-2-yl-2~{H}-pyrano[2,3-c]pyrazol-4-yl]-5-(trifluoromethyl)phenyl]phenyl]ethanoic acid
ChEMBL
DrugBank
ZINC
PDB chain5gvm Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5gvm Antimalarial Inhibitors Targeting Serine Hydroxymethyltransferase (SHMT) with in Vivo Efficacy and Analysis of their Binding Mode Based on X-ray Cocrystal Structures
Resolution2.24 Å
Binding residue
(original residue number in PDB)		L124 G128 H129 T183 K355 N356 T357
Binding residue
(residue number reindexed from 1)		L124 G128 H129 T183 K355 N356 T357
Annotation score1
Binding affinityMOAD: ic50=186nM
PDBbind-CN: -logKd/Ki=6.73,Kd=186nM
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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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5gvm, PDBe:5gvm, PDBj:5gvm
PDBsum5gvm
PubMed28537728
UniProtA5K8L9

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