Structure of PDB 6qvg Chain A Binding Site BS02

Receptor Information

>6qvg Chain A (length=453) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

WTGQESLSDSDPEMWELLQREKDRQCRGLELIASENFCSRAALEALGSCL
NNKYSEGYPGKRYYGGAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPYS
GSPANLAVYTALLQPHDRIMGLDLPDGGHLTHGYMSDVKRISATSIFFES
MPYKLNPKTGLIDYNQLALTARLFRPRLIIAGTSAYARLIDYARMREVCD
EVKAHLLADMAHISGLVAAKVIPSPFKHADIVTTTTHKTLRGARSGLIFY
RKGVKIPYTFEDRINFAVFPSLQGGPHNHAIAAVAVALKQACTPMFREYS
LQVLKNARAMADALLERGYSLVSGGTDNHLVLVDLRPKGLDGARAERVLE
LVSITANKNTCPGDRSAITPGGLRLGAPALTSRQFREDDFRRVVDFIDEG
VNIGLEVKSKTAKLQDFKSFLLKDSETSQRLANLRQRVEQFARAFPMPGF
DEH

Ligand information

Ligand ID

DDF

InChI

InChI=1S/C21H25N5O6/c22-21-25-17-14(19(30)26-21)9-12(10-23-17)2-1-11-3-5-13(6-4-11)18(29)24-15(20(31)32)7-8-16(27)28/h3-6,12,15H,1-2,7-10H2,(H,24,29)(H,27,28)(H,31,32)(H4,22,23,25,26,30)/t12-,15+/m1/s1

InChIKey

ZUQBAQVRAURMCL-DOMZBBRYSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	c1cc(ccc1CCC2CC3=C(NC2)NC(=NC3=O)N)C(=O)NC(CCC(=O)O)C(=O)O
CACTVS 3.341	NC1=NC(=O)C2=C(NC[C@H](CCc3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)C2)N1
ACDLabs 10.04	O=C(O)C(NC(=O)c1ccc(cc1)CCC3CNC=2NC(=NC(=O)C=2C3)N)CCC(=O)O
CACTVS 3.341	NC1=NC(=O)C2=C(NC[CH](CCc3ccc(cc3)C(=O)N[CH](CCC(O)=O)C(O)=O)C2)N1
OpenEye OEToolkits 1.5.0	c1cc(ccc1CC[C@@H]2CC3=C(NC2)NC(=NC3=O)N)C(=O)N[C@@H](CCC(=O)O)C(=O)O

Formula

C21 H25 N5 O6

Name

5,10-DIDEAZATETRAHYDROFOLIC ACID

PDB chain

6qvg Chain A Residue 607 [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	6qvg Structural basis of inhibition of the human serine hydroxymethyltransferase SHMT2 by antifolate drugs.
Resolution	2.32 Å
Binding residue (original residue number in PDB)	L166 G170 H171 L172 S226
Binding residue (residue number reindexed from 1)	L124 G128 H129 L130 S184
Annotation score	2

Enzymatic activity

Catalytic site (original residue number in PDB)	Y96 E98 D251 T277 K280 R286
Catalytic site (residue number reindexed from 1)	Y54 E56 D209 T235 K238 R244
Enzyme Commision number	2.1.2.1: glycine hydroxymethyltransferase.

Gene Ontology

	Molecular Function
GO:0003682	chromatin binding
GO:0004372	glycine hydroxymethyltransferase activity
GO:0005515	protein binding
GO:0008732	L-allo-threonine aldolase activity
GO:0016597	amino acid binding
GO:0016740	transferase activity
GO:0030170	pyridoxal phosphate binding
GO:0042802	identical protein binding

	Biological Process
GO:0002082	regulation of oxidative phosphorylation
GO:0006544	glycine metabolic process
GO:0006545	glycine biosynthetic process
GO:0006563	L-serine metabolic process
GO:0006564	L-serine biosynthetic process
GO:0006730	one-carbon metabolic process
GO:0008284	positive regulation of cell population proliferation
GO:0019264	glycine biosynthetic process from serine
GO:0034340	response to type I interferon
GO:0035999	tetrahydrofolate interconversion
GO:0046653	tetrahydrofolate metabolic process
GO:0051262	protein tetramerization
GO:0051289	protein homotetramerization
GO:0070129	regulation of mitochondrial translation
GO:0070536	protein K63-linked deubiquitination
GO:1903715	regulation of aerobic respiration

	Cellular Component
GO:0005634	nucleus
GO:0005737	cytoplasm
GO:0005739	mitochondrion
GO:0005743	mitochondrial inner membrane
GO:0005759	mitochondrial matrix
GO:0015630	microtubule cytoskeleton
GO:0042645	mitochondrial nucleoid
GO:0070062	extracellular exosome
GO:0070552	BRISC complex

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Molecular Function

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Cellular Component

External links

PDB	RCSB:6qvg, PDBe:6qvg, PDBj:6qvg
PDBsum	6qvg
PubMed	31127856
UniProt	P34897\|GLYM_HUMAN Serine hydroxymethyltransferase, mitochondrial (Gene Name=SHMT2)

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