Structure of PDB 4jdw Chain A Binding Site BS01

Receptor Information
>4jdw Chain A (length=360) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
CPVSSYNEWDPLEEVIVGRAENACVPPFTIEVKANTYEKYWPFYQKQGGH
YFPKDHLKKAVAEIEEMCNILKTEGVTVRRPDPIDWSLKYKTPDFESTGL
YSAMPRDILIVVGNEIIEAPMAWRSRFFEYRAYRSIIKDYFHRGAKWTTA
PKPTMADELYNQDYPIHSVEDRHKLAAQGKFVTTEFEPCFDAADFIRAGR
DIFAQRSQVTNYLGIEWMRRHLAPDYRVHIISFKDPNPMHIDATFNIIGP
GIVLSNPDRPCHQIDLFKKAGWTIITPPTPIIPDDHPLWMSSKWLSMNVL
MLDEKRVMVDANEVPIQKMFEKLGITTIKVNIRNANSLGGGFHAWTCDVR
RRGTLQSYLD
Ligand information
Ligand IDARG
InChIInChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/p+1/t4-/m0/s1
InChIKeyODKSFYDXXFIFQN-BYPYZUCNSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(CC(C(=O)O)N)CNC(=[NH2+])N
CACTVS 3.341N[C@@H](CCCNC(N)=[NH2+])C(O)=O
OpenEye OEToolkits 1.5.0C(C[C@@H](C(=O)O)N)CNC(=[NH2+])N
CACTVS 3.341N[CH](CCCNC(N)=[NH2+])C(O)=O
ACDLabs 10.04O=C(O)C(N)CCCN\C(=[NH2+])N
FormulaC6 H15 N4 O2
NameARGININE
ChEMBL
DrugBank
ZINC
PDB chain4jdw Chain A Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4jdw Crystal structure and mechanism of human L-arginine:glycine amidinotransferase: a mitochondrial enzyme involved in creatine biosynthesis.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		D170 M302 H303 D305 A306 R322 S354 S355 A407
Binding residue
(residue number reindexed from 1)		D107 M239 H240 D242 A243 R259 S291 S292 A344
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) E71 D170 D254 H303 D305 N361 H406 A407
Catalytic site (residue number reindexed from 1) E8 D107 D191 H240 D242 N298 H343 A344
Enzyme Commision number 2.1.4.1: glycine amidinotransferase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0015067 amidinotransferase activity
GO:0015068 glycine amidinotransferase activity
GO:0016740 transferase activity
Biological Process
GO:0006600 creatine metabolic process
GO:0006601 creatine biosynthetic process
GO:0007611 learning or memory
GO:0014889 muscle atrophy
GO:0120162 positive regulation of cold-induced thermogenesis
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005758 mitochondrial intermembrane space
GO:0070062 extracellular exosome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4jdw, PDBe:4jdw, PDBj:4jdw
PDBsum4jdw
PubMed9218780
UniProtP50440|GATM_HUMAN Glycine amidinotransferase, mitochondrial (Gene Name=GATM)

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