Structure of PDB 7dd5 Chain B Binding Site BS04

Receptor Information

>7dd5 Chain B (length=799) Species: 9031 (Gallus gallus)

PNQRAQKKGDIILGGLFPIHFGVAAKDQDLKSRPESVECIRYNFRGFRWL
QAMIFAIEEINNSPNLLPNMTLGYRIFDTCNTVSKALEATLSFVAQNKID
SPSTIAVVGATGSGVSTAVANLLGLFYIPQVSYASSSRLLSNKNQFKSFL
RTIPNDEHQATAMADIIEYFRWNWVGTIAADDDYGRPGIEKFREEAEERD
ICIDFSELISQYSDEEEIQQVVEVIQNSTARVIVVFSSGPDLEPLIKEIV
RRNITGKIWLASEAWASSSLIAMPEFFRVIGSTIGFALKAGQIPGFREFL
QKVHPKKSANNGFAKEFWEETFNCYLRPPCTGDENITSVETPYMDFTHLR
ISYNVYLAVYSIAHALQDIYTCTPGKGLFTNGSCADIKKVEAWQVLKHLR
HLNFTSNMGEQVDFDEFGDLVGNYSIINWHLSPEDGSVVFEEVGHYNVYA
KKGERLFINENKILWSGFSKEVPFSNCSRDCLPGTRKGIIEGEPTCCFEC
VDCPDGEYSDETDASACDKCPEDYWSNENHTSCIPKQIEFLSWTEPFGIA
LTLFAVLGIFLTSFVLGVFTKFRNTPIVKATNRELSYLLLFSLLCCFSSS
LFFIGEPQNWTCRLRQPAFGISFVLCISCILVKTNRVLLVFETSLHRKWW
GLNLQFLLVFLCTFVQIVICVIWLYTAPPSSYRNHELEDEIIFITCHEGS
LMALGFLIGYTCLLAAICFFFAFKSRKLPENFNEAKFITFSMLIFFIVWI
SFIPAYASTYGKFVSAVEVIAILAASFGLLACIFFNKVYIILFKPSRNT

Ligand information

• Ligand ID: YP1
• InChI: InChI=1S/C24H25ClN2O2/c1-24(2,13-17-10-11-18-6-3-4-7-19(18)12-17)27-15-20(28)16-29-23-9-5-8-22(25)21(23)14-26/h3-12,20,27-28H,13,15-16H2,1-2H3/t20-/m1/s1
• InChIKey: PZUJQWHTIRWCID-HXUWFJFHSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC(C)(Cc1ccc2ccccc2c1)NCC(COc3cccc(c3C#N)Cl)O
  ACDLabs 12.01: N#Cc1c(cccc1Cl)OCC(O)CNC(C)(C)Cc1cc2ccccc2cc1
  OpenEye OEToolkits 2.0.7: CC(C)(Cc1ccc2ccccc2c1)NC[C@H](COc3cccc(c3C#N)Cl)O
  CACTVS 3.385: CC(C)(Cc1ccc2ccccc2c1)NC[CH](O)COc3cccc(Cl)c3C#N
  CACTVS 3.385: CC(C)(Cc1ccc2ccccc2c1)NC[C@@H](O)COc3cccc(Cl)c3C#N
• Formula: C24 H25 Cl N2 O2
• Name: 2-chloro-6-[(2R)-2-hydroxy-3-{[2-methyl-1-(naphthalen-2-yl)propan-2-yl]amino}propoxy]benzonitrile
• ChEMBL: CHEMBL180672
• DrugBank: DB05695
• ZINC: ZINC000003975668
• PDB chain: 7dd5 Chain B Residue 1108

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7dd5 Structural basis for activation and allosteric modulation of full-length calcium-sensing receptor.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): F683 I776 W817 Y824 E836
• Binding residue (residue number reindexed from 1): F619 I708 W749 Y756 E768
• Annotation score: 1

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Tue Feb 18 05:24:04 2025

A problem occurred in a Python script. Here is the sequence of function calls leading up to the error, in the order they occurred.

 /var/www/html/BioLiP/pdb.cgi in <module>()

   1435     title=pdb2title(pdbid)

   1436     if bs.startswith("BS"):

=> 1437         pubmed,uniprot=display_interaction(pdbid,asym_id,bs,title)

   1438     else:

   1439         if lig3:

pubmed = '', uniprot = '', display_interaction = <function display_interaction>, pdbid = '7dd5', asym_id = 'B', bs = 'BS04', title = 'Structural basis for activation and allosteric modulation of full-length calcium-sensing receptor.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='7dd5', asym_id='B', bs='BS04', title='Structural basis for activation and allosteric modulation of full-length calcium-sensing receptor.')

   1295         display_ec(ec,csaOrig,csaRenu)

   1296     if go:

=> 1297         display_go(go,uniprot,pdbid,asym_id)

   1298     return pubmed,uniprot

   1299 

global display_go = <function display_go>, go = '0004930,0007186,0016020', uniprot = '', pdbid = '7dd5', asym_id = 'B'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0004930,0007186,0016020', uniprot='', pdbid='7dd5', asym_id='B')

    480         '''.replace("$namespace_link",namespace_link

    481           ).replace("$namespace",namespace

=>  482           ).replace("$uniprot",u

    483         ))

    484         for l,(term,name) in enumerate(go2aspect[Aspect]):

u undefined

UnboundLocalError: local variable 'u' referenced before assignment
      args = ("local variable 'u' referenced before assignment",)
      with_traceback = <built-in method with_traceback of UnboundLocalError object>