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Structure of PDB 1c9y Chain A Binding Site BS01

Receptor Information

>1c9y Chain A (length=321) Species: 9606 (Homo sapiens)

KVQLKGRDLLTLKNFTGEEIKYMLWLSADLKFRIKQKGEYLPLLQGKSLG
MIFEKRSTRTRLSTETGFALLGGHPCFLTTQDIHLGVNESLTDTARVLSS
MADAVLARVYKQSDLDTLAKEASIPIINGLSDLYHPIQILADYLTLQEHY
SSLKGLTLSWIGDGNNILHSIMMSAAKFGMHLQAATPKGYEPDASVTKLA
EQYAKENGTKLLLTNDPLEAAHGGNVLITDTWISMGREEEKKKRLQAFQG
YQVTMKTAKVAASDWTFLHCLPRKPEEVDDEVFYSPRSLVFPEAENRKWT
IMAVMVSLLTDYSPQLQKPKF

Ligand information

• Ligand ID: NVA
• InChI: InChI=1S/C5H11NO2/c1-2-3-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m0/s1
• InChIKey: SNDPXSYFESPGGJ-BYPYZUCNSA-N
• SMILES:
  CACTVS 3.341: CCC[CH](N)C(O)=O
  CACTVS 3.341: CCC[C@H](N)C(O)=O
  OpenEye OEToolkits 1.5.0: CCC[C@@H](C(=O)O)N
  ACDLabs 10.04: O=C(O)C(N)CCC
  OpenEye OEToolkits 1.5.0: CCCC(C(=O)O)N
• Formula: C5 H11 N O2
• Name: NORVALINE
• ChEMBL: CHEMBL55612
• DrugBank: DB04185
• ZINC: ZINC000000391821
• PDB chain: 1c9y Chain A Residue 355

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1c9y Crystal structure of human ornithine transcarbamylase complexed with carbamoyl phosphate and L-norvaline at 1.9 A resolution.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): L163 N199 D263 S267 M268
• Binding residue (residue number reindexed from 1): L130 N166 D230 S234 M235
• Annotation score: 2

Enzymatic activity

• Catalytic site (original residue number in PDB): R92 T93 V120 R141 H168 Q171 D263 C303 R330
• Catalytic site (residue number reindexed from 1): R59 T60 V87 R108 H135 Q138 D230 C270 R297
• Enzyme Commision number: 2.1.3.3: ornithine carbamoyltransferase.

Gene Ontology

Molecular Function

• GO:0004585 ornithine carbamoyltransferase activity
• GO:0005543 phospholipid binding
• GO:0016597 amino acid binding
• GO:0016740 transferase activity
• GO:0016743 carboxyl- or carbamoyltransferase activity
• GO:0042301 phosphate ion binding
• GO:0042802 identical protein binding

Biological Process

• GO:0000050 urea cycle
• GO:0001889 liver development
• GO:0006520 amino acid metabolic process
• GO:0006526 L-arginine biosynthetic process
• GO:0006591 ornithine metabolic process
• GO:0006593 ornithine catabolic process
• GO:0007494 midgut development
• GO:0009410 response to xenobiotic stimulus
• GO:0010043 response to zinc ion
• GO:0019240 citrulline biosynthetic process
• GO:0031667 response to nutrient levels
• GO:0032868 response to insulin
• GO:0042450 arginine biosynthetic process via ornithine
• GO:0055081 monoatomic anion homeostasis
• GO:0070781 response to biotin
• GO:0097272 ammonium homeostasis

Cellular Component

• GO:0005739 mitochondrion
• GO:0005743 mitochondrial inner membrane
• GO:0005759 mitochondrial matrix

External links

• PDB: RCSB:1c9y, PDBe:1c9y, PDBj:1c9y
• PDBsum: 1c9y
• PubMed: 10813810
• UniProt: P00480|OTC_HUMAN Ornithine transcarbamylase, mitochondrial (Gene Name=OTC)

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