Structure of PDB 4tmr Chain B Binding Site BS03

Receptor Information
>4tmr Chain B (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 ID99S
InChIInChI=1S/C24H21N5O3S/c1-12(2)24(17(11-26)21(27)32-22-20(24)13(3)28-29-22)16-8-14(10-25)7-15(9-16)18-5-6-19(33-18)23(30)31-4/h5-9,12H,27H2,1-4H3,(H,28,29)/t24-/m0/s1
InChIKeyCTJJXDPGSNOYMV-DEOSSOPVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2Cc1c2c(n[nH]1)OC(=C(C2(c3cc(cc(c3)c4ccc(s4)C(=O)OC)C#N)C(C)C)C#N)N
CACTVS 3.385COC(=O)c1sc(cc1)c2cc(cc(c2)[C]3(C(C)C)C(=C(N)Oc4n[nH]c(C)c34)C#N)C#N
ACDLabs 12.01N#CC2=C(Oc1nnc(c1C2(c4cc(C#N)cc(c3sc(C(=O)OC)cc3)c4)C(C)C)C)N
OpenEye OEToolkits 1.9.2Cc1c2c(n[nH]1)OC(=C([C@@]2(c3cc(cc(c3)c4ccc(s4)C(=O)OC)C#N)C(C)C)C#N)N
CACTVS 3.385COC(=O)c1sc(cc1)c2cc(cc(c2)[C@@]3(C(C)C)C(=C(N)Oc4n[nH]c(C)c34)C#N)C#N
FormulaC24 H21 N5 O3 S
Namemethyl 5-{3-[(4S)-6-amino-5-cyano-3-methyl-4-(propan-2-yl)-2,4-dihydropyrano[2,3-c]pyrazol-4-yl]-5-cyanophenyl}thiophene-2-carboxylate
ChEMBL
DrugBank
ZINCZINC000263620321
PDB chain4tmr Chain B Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4tmr Inhibitors of Plasmodial Serine Hydroxymethyltransferase (SHMT): Cocrystal Structures of Pyrazolopyrans with Potent Blood- and Liver-Stage Activities.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		L124 G128 H129 L130 V141 T183 N356 C364 R371
Binding residue
(residue number reindexed from 1)		L124 G128 H129 L130 V141 T183 N356 C364 R371
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.22,IC50=60nM
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:4tmr, PDBe:4tmr, PDBj:4tmr
PDBsum4tmr
PubMed25785478
UniProtA5K8L9

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