Structure of PDB 5yg3 Chain B Binding Site BS04

Receptor Information
>5yg3 Chain B (length=442) Species: 5855 (Plasmodium vivax) [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 ID8UC
InChIInChI=1S/C23H20FN5O/c1-12-19-21(29-28-12)30-20(26)17(11-25)23(19)16-8-14(13-4-6-27-7-5-13)9-18(24)15(16)10-22(23,2)3/h4-9H,10,26H2,1-3H3,(H,28,29)/t23-/m1/s1
InChIKeyQSHPRVNBDFMPTJ-HSZRJFAPSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1[nH]nc2OC(=C(C#N)[C@]3(c4cc(cc(F)c4CC3(C)C)c5ccncc5)c12)N
CACTVS 3.385Cc1[nH]nc2OC(=C(C#N)[C]3(c4cc(cc(F)c4CC3(C)C)c5ccncc5)c12)N
OpenEye OEToolkits 2.0.6Cc1c2c(n[nH]1)OC(=C([C@]23c4cc(cc(c4CC3(C)C)F)c5ccncc5)C#N)N
OpenEye OEToolkits 2.0.6Cc1c2c(n[nH]1)OC(=C(C23c4cc(cc(c4CC3(C)C)F)c5ccncc5)C#N)N
FormulaC23 H20 F N5 O
Name(3~{S})-6'-azanyl-7-fluoranyl-2,2,3'-trimethyl-5-pyridin-4-yl-spiro[1~{H}-indene-3,4'-2~{H}-pyrano[2,3-c]pyrazole]-5'-carbonitrile
ChEMBL
DrugBank
ZINC
PDB chain5yg3 Chain B Residue 502 [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]
PDB5yg3 Potent Inhibitors of Plasmodial Serine Hydroxymethyltransferase (SHMT) Featuring a Spirocyclic Scaffold
Resolution2.4 Å
Binding residue
(original residue number in PDB)		L124 G128 H129 L130 T183 K355 C364
Binding residue
(residue number reindexed from 1)		L124 G128 H129 L130 T183 K355 C364
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.85,IC50=0.014uM
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:0008168 methyltransferase activity
GO:0008270 zinc ion binding
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:0032259 methylation
GO:0035999 tetrahydrofolate interconversion
GO:0046653 tetrahydrofolate metabolic process
GO:0046655 folic acid metabolic process
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5yg3, PDBe:5yg3, PDBj:5yg3
PDBsum5yg3
PubMed29655285
UniProtA0A1G4H5I1

[Back to BioLiP]