Structure of PDB 6zis Chain A Binding Site BS03

Receptor Information
>6zis Chain A (length=569) Species: 9606,1327989 [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SAKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFP
QVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVR
YNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALM
FNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDL
IKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLP
TFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKP
LGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVI
NAASGRQTVDEALKDAQTNAAAEFTTACQEANYGALLRELCLTQFQVDME
AVGETLWCDWGRTIRSYRELADCTWHMAEKLGCFWPNAEVDRFFLAVHGR
YFRSCPISIQLGVTRNKIMTAQYECYQKIMQDPIQQGVYCQRTWDGWLCW
NDVAAGTESMQLCPDYFQDFDPSEKVTKICDQDGNWFRHPASQRTWTDYT
QCNVNTHEKVKTALNLFYL
Ligand information
Ligand ID3N6
InChIInChI=1S/C38H47Br2N9O5/c39-29-21-25(22-30(40)34(29)50)23-33(45-37(53)48-15-10-28(11-16-48)49-24-26-5-1-2-6-31(26)44-38(49)54)35(51)43-32(7-3-4-12-41)36(52)47-19-17-46(18-20-47)27-8-13-42-14-9-27/h1-2,5-6,8-9,13-14,21-22,28,32-33,50H,3-4,7,10-12,15-20,23-24,41H2,(H,43,51)(H,44,54)(H,45,53)/t32-,33+/m0/s1
InChIKeyITIXDWVDFFXNEG-JHOUSYSJSA-N
SMILES
SoftwareSMILES
CACTVS 3.370NCCCC[CH](NC(=O)[CH](Cc1cc(Br)c(O)c(Br)c1)NC(=O)N2CC[CH](CC2)N3Cc4ccccc4NC3=O)C(=O)N5CCN(CC5)c6ccncc6
CACTVS 3.370NCCCC[C@H](NC(=O)[C@@H](Cc1cc(Br)c(O)c(Br)c1)NC(=O)N2CC[C@@H](CC2)N3Cc4ccccc4NC3=O)C(=O)N5CCN(CC5)c6ccncc6
OpenEye OEToolkits 1.7.0c1ccc2c(c1)CN(C(=O)N2)C3CCN(CC3)C(=O)N[C@H](Cc4cc(c(c(c4)Br)O)Br)C(=O)N[C@@H](CCCCN)C(=O)N5CCN(CC5)c6ccncc6
OpenEye OEToolkits 1.7.0c1ccc2c(c1)CN(C(=O)N2)C3CCN(CC3)C(=O)NC(Cc4cc(c(c(c4)Br)O)Br)C(=O)NC(CCCCN)C(=O)N5CCN(CC5)c6ccncc6
ACDLabs 12.01O=C(N2CCN(c1ccncc1)CC2)C(NC(=O)C(NC(=O)N5CCC(N4C(=O)Nc3c(cccc3)C4)CC5)Cc6cc(Br)c(O)c(Br)c6)CCCCN
FormulaC38 H47 Br2 N9 O5
NameN-{(1S)-5-amino-1-[(4-pyridin-4-ylpiperazin-1-yl)carbonyl]pentyl}-3,5-dibromo-Nalpha-{[4-(2-oxo-1,4-dihydroquinazolin-3 (2H)-yl)piperidin-1-yl]carbonyl}-D-tyrosinamide;
Olcegepant
ChEMBLCHEMBL207197
DrugBankDB04869
ZINCZINC000098052868
PDB chain6zis Chain A Residue 2204 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6zis Structure-Based Drug Discovery ofN-((R)-3-(7-Methyl-1H-indazol-5-yl)-1-oxo-1-(((S)-1-oxo-3-(piperidin-4-yl)-1-(4-(pyridin-4-yl)piperazin-1-yl)propan-2-yl)amino)propan-2-yl)-2'-oxo-1',2'-dihydrospiro[piperidine-4,4'-pyrido[2,3-d][1,3]oxazine]-1-carboxamide (HTL22562): A Calcitonin Gene-Related Peptide Receptor Antagonist for Acute Treatment of Migraine.
Resolution1.73 Å
Binding residue
(original residue number in PDB)		A1070 D1071 W1074 W1084 R2038 I2041 M2042 D2070 G2071 W2072 F2092 D2094 W2121 T2122 Y2124
Binding residue
(residue number reindexed from 1)		A421 D422 W425 W435 R465 I468 M469 D495 G496 W497 F517 D519 W546 T547 Y549
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0004930 G protein-coupled receptor activity
GO:0015026 coreceptor activity
GO:0015144 carbohydrate transmembrane transporter activity
Biological Process
GO:0006886 intracellular protein transport
GO:0007186 G protein-coupled receptor signaling pathway
GO:0008277 regulation of G protein-coupled receptor signaling pathway
GO:0008643 carbohydrate transport
GO:0055085 transmembrane transport
Cellular Component
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6zis, PDBe:6zis, PDBj:6zis
PDBsum6zis
PubMed32558564
UniProtA0A4P1LXE0;
O60894|RAMP1_HUMAN Receptor activity-modifying protein 1 (Gene Name=RAMP1);
Q16602|CALRL_HUMAN Calcitonin gene-related peptide type 1 receptor (Gene Name=CALCRL)

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