Structure of PDB 3gki Chain A Binding Site BS01

Receptor Information

>3gki Chain A (length=225) Species: 9606 (Homo sapiens)

QSCVWYGECGIAYGDKRYNCEYSGPPKPLPKDGYDLVQELCPGFFFGQVS
LCCDVRQLQTLKDNLQLPLQFLSRCPSCFYNLLNLFCELTCSPRQSQFLQ
VTATEDYVDPVTNQTKTNVKELQYYVGQSFANAMYNACRDVEAPSSNDKA
LGLLCGKDADACQATNWIEYMFNKDNGQAPFTITPVFSDFPVHGMEPMNN
ATKGCDESVDEVTAPCSCQDCSIVC

Ligand information

• Ligand ID: CLR
• InChI: InChI=1S/C27H46O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h9,18-19,21-25,28H,6-8,10-17H2,1-5H3/t19-,21+,22+,23-,24+,25+,26+,27-/m1/s1
• InChIKey: HVYWMOMLDIMFJA-DPAQBDIFSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC(C)CCCC(C)C1CCC2C1(CCC3C2CC=C4C3(CCC(C4)O)C)C
  CACTVS 3.341: CC(C)CCC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC=C4C[C@@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
  ACDLabs 10.04: OC4CCC3(C(=CCC2C1C(C(C(C)CCCC(C)C)CC1)(C)CCC23)C4)C
  OpenEye OEToolkits 1.5.0: CC(C)CCC[C@@H](C)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3[C@H]2CC=C4[C@@]3(CC[C@@H](C4)O)C)C
  CACTVS 3.341: CC(C)CCC[CH](C)[CH]1CC[CH]2[CH]3CC=C4C[CH](O)CC[C]4(C)[CH]3CC[C]12C
• Formula: C27 H46 O
• Name: CHOLESTEROL
• ChEMBL: CHEMBL112570
• DrugBank: DB04540
• ZINC: ZINC000003875383
• PDB chain: 3gki Chain A Residue 253

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3gki Structure of N-terminal domain of NPC1 reveals distinct subdomains for binding and transfer of cholesterol.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): N41 Q79 L83 N86 P90 F108 T112 L176 Y192 M193 A201 P202 F203
• Binding residue (residue number reindexed from 1): N19 Q57 L61 N64 P68 F86 T90 L154 Y170 M171 A179 P180 F181
• Annotation score: 5

External links

• PDB: RCSB:3gki, PDBe:3gki, PDBj:3gki
• PDBsum: 3gki
• PubMed: 19563754
• UniProt: O15118|NPC1_HUMAN NPC intracellular cholesterol transporter 1 (Gene Name=NPC1)