Structure of PDB 3jdw Chain A Binding Site BS01

Receptor Information
>3jdw 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
MLDEKRVMVDANEVPIQKMFEKLGITTIKVNIRNANSLGGGFHCWTCDVR
RRGTLQSYLD
Ligand information
Ligand IDORN
InChIInChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m0/s1
InChIKeyAHLPHDHHMVZTML-BYPYZUCNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C(C[C@@H](C(=O)O)N)CN
CACTVS 3.370NCCC[CH](N)C(O)=O
CACTVS 3.370NCCC[C@H](N)C(O)=O
ACDLabs 12.01O=C(O)C(N)CCCN
OpenEye OEToolkits 1.7.6C(CC(C(=O)O)N)CN
FormulaC5 H12 N2 O2
NameL-ornithine
ChEMBLCHEMBL446143
DrugBankDB00129
ZINCZINC000001532530
PDB chain3jdw 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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PDB3jdw Crystal structure and mechanism of human L-arginine:glycine amidinotransferase: a mitochondrial enzyme involved in creatine biosynthesis.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		M302 H303 A306 R322 S354 S355 C407
Binding residue
(residue number reindexed from 1)		M239 H240 A243 R259 S291 S292 C344
Annotation score5
Binding affinityMOAD: Ki=253uM
PDBbind-CN: -logKd/Ki=3.60,Ki=253uM
Enzymatic activity
Catalytic site (original residue number in PDB) E71 D170 D254 H303 D305 N361 H406 C407
Catalytic site (residue number reindexed from 1) E8 D107 D191 H240 D242 N298 H343 C344
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

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3jdw, PDBe:3jdw, PDBj:3jdw
PDBsum3jdw
PubMed9218780
UniProtP50440|GATM_HUMAN Glycine amidinotransferase, mitochondrial (Gene Name=GATM)

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