Structure of PDB 1ls3 Chain C Binding Site BS04

Receptor Information
>1ls3 Chain C (length=465) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALWSSHEQMLAQPLKDSDAEVYDIIKKESNRQRVGLELIASENFASRAVL
EALGSCLNNKYSEGYPGQRYYGGTEHIDELETLCQKRALQAYGLDPQCWG
VNVQPYSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISA
TSIFFESMAYKVNPDTGYIDYDRLEENARLFHPKLIIAGTSCYSRNLDYG
RLRKIADENGAYLMADMAHISGLVVAGVVPSPFEHCHVVTTTTHKTLRGC
RAGMIFYRRGVRKEILYNLESLINSAVFPGLQGGPHNHAIAGVAVALKQA
MTPEFKEYQRQVVANCRALSAALVELGYKIVTGGSDNHLILVDLRSKGTD
GGRAEKVLEACSIACNKNTCPGDKSALRPSGLRLGTPALTSRGLLEKDFQ
KVAHFIHRGIELTVQIQDDTGPRATLKEFKEKLAGDEKHQRAVRALRQEV
ESFAALFPLPGLPGF
Ligand information
Ligand IDTGF
InChIInChI=1S/C30H37N9O13/c31-30-37-24-23(26(46)38-30)39(13-40)16(12-33-24)11-32-15-3-1-14(2-4-15)25(45)36-19(29(51)52)6-9-21(42)34-17(27(47)48)5-8-20(41)35-18(28(49)50)7-10-22(43)44/h1-4,13,16-19,32H,5-12H2,(H,34,42)(H,35,41)(H,36,45)(H,43,44)(H,47,48)(H,49,50)(H,51,52)(H4,31,33,37,38,46)/t16-,17-,18-,19-/m0/s1
InChIKeyZLOMJLIQXBKNHU-VJANTYMQSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC2=C(N(C=O)[CH](CNc3ccc(cc3)C(=O)N[CH](CCC(=O)N[CH](CCC(=O)N[CH](CCC(O)=O)C(O)=O)C(O)=O)C(O)=O)CN2)C(=O)N1
CACTVS 3.341NC1=NC2=C(N(C=O)[C@@H](CNc3ccc(cc3)C(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)N[C@@H](CCC(O)=O)C(O)=O)C(O)=O)C(O)=O)CN2)C(=O)N1
ACDLabs 10.04O=C(O)C(NC(=O)CCC(C(=O)O)NC(=O)CCC(C(=O)O)NC(=O)c1ccc(cc1)NCC2N(C=3C(=O)NC(=NC=3NC2)N)C=O)CCC(=O)O
OpenEye OEToolkits 1.5.0c1cc(ccc1C(=O)NC(CCC(=O)NC(CCC(=O)NC(CCC(=O)O)C(=O)O)C(=O)O)C(=O)O)NCC2CNC3=C(N2C=O)C(=O)NC(=N3)N
OpenEye OEToolkits 1.5.0c1cc(ccc1C(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)O)C(=O)O)C(=O)O)C(=O)O)NC[C@H]2CNC3=C(N2C=O)C(=O)NC(=N3)N
FormulaC30 H37 N9 O13
Name2-[4-(4-{4-[(2-AMINO-5-FORMYL-4-OXO-3,4,5,6,7,8-HEXAHYDRO-PTERIDIN-6-YLMETHYL)-AMINO]-BENZOYLAMINO}-4-CARBOXY-BUTYRYLAM INO)-4-CARBOXY-BUTYRYLAMINO]-PENTANEDIOIC ACID;
TRIGLU-5-FORMYL-TETRAHYDROFOLATE
ChEMBLCHEMBL1236268
DrugBankDB02067
ZINCZINC000055398661
PDB chain1ls3 Chain D Residue 420F [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]
PDB1ls3 Location of the Pteroylpolyglutamate Binding Site on Rabbit Cytosolic Serine Hydroxymethyltransferase
Resolution2.7 Å
Binding residue
(original residue number in PDB)		E57 Y64 Y65
Binding residue
(residue number reindexed from 1)		E63 Y70 Y71
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) Y55 E57 D200 T226 K229 R235
Catalytic site (residue number reindexed from 1) Y61 E63 D216 T242 K245 R251
Enzyme Commision number 2.1.2.1: glycine hydroxymethyltransferase.
Gene Ontology
Molecular Function
GO:0000900 mRNA regulatory element binding translation repressor activity
GO:0004372 glycine hydroxymethyltransferase activity
GO:0008270 zinc ion binding
GO:0016740 transferase activity
GO:0030170 pyridoxal phosphate binding
GO:0036094 small molecule binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0048027 mRNA 5'-UTR binding
GO:0050897 cobalt ion binding
GO:0070905 serine binding
Biological Process
GO:0006544 glycine metabolic process
GO:0006563 L-serine metabolic process
GO:0006565 L-serine catabolic process
GO:0006730 one-carbon metabolic process
GO:0009113 purine nucleobase biosynthetic process
GO:0017148 negative regulation of translation
GO:0019264 glycine biosynthetic process from serine
GO:0035999 tetrahydrofolate interconversion
GO:0046653 tetrahydrofolate metabolic process
GO:0046655 folic acid metabolic process
GO:0051289 protein homotetramerization
GO:1904482 cellular response to tetrahydrofolate
GO:1990830 cellular response to leukemia inhibitory factor
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1ls3, PDBe:1ls3, PDBj:1ls3
PDBsum1ls3
PubMed12438316
UniProtP07511|GLYC_RABIT Serine hydroxymethyltransferase, cytosolic (Gene Name=SHMT1)

[Back to BioLiP]