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(-) Description

Title :  STRUCTURE OF PD-L1/SMALL-MOLECULE INHIBITOR COMPLEX
 
Authors :  K. Guzik, K. M. Zak, P. Grudnik, G. Dubin, T. A. Holak
Date :  07 Feb 17  (Deposition) - 28 Jun 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pd-L1, Pd-1, Small-Molecule Inhibitor, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Guzik, K. M. Zak, P. Grudnik, K. Magiera, B. Musielak, R. Torner, L. Skalniak, A. Domling, G. Dubin, T. A. Holak
Small-Molecule Inhibitors Of The Programmed Cell Death-1/Programmed Death-Ligand 1 (Pd-1/Pd-L1) Interaction Via Transiently-Induced Protein States And Dimerization Of Pd-L1.
J. Med. Chem. 2017
PubMed-ID: 28613862  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.7B00293

(-) Compounds

Molecule 1 - PROGRAMMED CELL DEATH 1 LIGAND 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneCD274, B7H1, PDCD1L1, PDCD1LG1, PDL1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPROGRAMMED DEATH LIGAND 1,B7 HOMOLOG 1,B7-H1
 
Molecule 2 - PROGRAMMED CELL DEATH 1 LIGAND 1
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneCD274, B7H1, PDCD1L1, PDCD1LG1, PDL1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPROGRAMMED DEATH LIGAND 1,B7 HOMOLOG 1,B7-H1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
18HW1Ligand/Ion4-[[4-[[3-(2,3-DIHYDRO-1,4-BENZODIOXIN-6-YL)-2-METHYL-PHENYL]METHOXY]-2,5-BIS(FLUORANYL)PHENYL]METHYLAMINO]-3-OXIDANYLIDENE-BUTANOIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:19 , THR A:20 , ILE A:54 , TYR A:56 , MET A:115 , ALA A:121 , ASP A:122 , HOH A:229 , ILE B:54 , TYR B:56 , GLN B:66 , VAL B:68 , MET B:115 , ILE B:116 , SER B:117 , ALA B:121 , ASP B:122 , HOH B:306 , HOH B:316binding site for residue 8HW B 201

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:40 -A:114
2B:40 -B:114

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:74 -Lys A:75

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5N2F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5N2F)

(-) Exons   (0, 0)

(no "Exon" information available for 5N2F)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:126
                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeee....eeeeee.......hhhh.eeeeee..eeeeeee..ee.....hhhhh..eee.hhhhhh.eeeeee...hhhhheeeeeeee...eeeeeeeeeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5n2f A  18 AFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYAAALEHHHH 143
                                    27        37        47        57        67        77        87        97       107       117       127       137      

Chain B from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee....eee..........hhhh.eeeeee..eeeeeee....hhhhhhhhhh..eee.hhhhhhh...eee...hhhhheeeeeeee...eeeeeeeeeee.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 5n2f B  18 AFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYAAALEHH 141
                                    27        37        47        57        67        77        87        97       107       117       127       137    

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5N2F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5N2F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5N2F)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PD1L1_HUMAN | Q9NZQ73bik 3bis 3fn3 3sbw 4z18 4zqk 5c3t 5ggt 5grj 5ius 5j89 5j8o 5jdr 5jds 5n2d

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5N2F)