Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T99948 | Target Info | |||
| Target Name | Programmed cell death 1 ligand 1 (PD-L1) | ||||
| Synonyms | hPD-L1; Programmed death ligand 1; PDL1; PDCD1LG1; PDCD1L1; PDCD1 ligand 1; B7H1; B7-H1; B7 homolog 1 | ||||
| Target Type | Successful Target | ||||
| Gene Name | CD274 | ||||
| Biochemical Class | Immunoglobulin | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: PMID30107136-Compound-Example1 | Ligand Info | |||||
| Structure Description | Structure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass inhibitor | PDB:5J89 | ||||
| Method | X-ray diffraction | Resolution | 2.20 Å | Mutation | No | [1] |
| PDB Sequence |
AFTVTVPKDL
27 YVVEYGSNMT37 IECKFPVEKQ47 LDLAALIVYW57 EMEDKNIIQF67 VHGEEDLKVQ 77 HSSYRQRARL87 LKDQLSLGNA97 ALQITDVKLQ107 DAGVYRCMIS117 YGGADYKRIT 127 VKVNAPYAAA137 LEHHH
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| Ligand Name: N-({2,6-dimethoxy-4-[(2-methyl[1,1'-biphenyl]-3-yl)methoxy]phenyl}methyl)-D-alanine | Ligand Info | |||||
| Structure Description | IgV-V76T BMS compound 105 | PDB:6NM8 | ||||
| Method | X-ray diffraction | Resolution | 2.79 Å | Mutation | Yes | [2] |
| PDB Sequence |
AFTVTVPKDL
27 YVVEYGSNMT37 IECKFPVEKQ47 LDLAALIVYW57 EMEDKNIIQF67 VHGEEDLKTQ 77 HSSYRQRARL87 LKDQLSLGNA97 ALQITDVKLQ107 DAGVYRCMIS117 YGGADYKRIT 127 VKVNAPYAAA137 LEHHH
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| Ligand Name: (2~{R})-2-[[2-[(3-cyanophenyl)methoxy]-4-[[3-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-methyl-phenyl]methoxy]-5-methyl-phenyl]methylamino]-3-oxidanyl-propanoic acid | Ligand Info | |||||
| Structure Description | Structure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass inhibitor | PDB:5NIU | ||||
| Method | X-ray diffraction | Resolution | 2.01 Å | Mutation | No | [3] |
| PDB Sequence |
AFTVTVPKDL
27 YVVEYGSNMT37 IECKFPVEKQ47 LDLAALIVYW57 EMEDKNIIQF67 VHGEEDLKVQ 77 HSSYRQRARL87 LKDQLSLGNA97 ALQITDVKLQ107 DAGVYRCMIS117 YGGADYKRIT 127 VKVNAPYAAA137 LEHHHH
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8YZ or .8YZ2 or .8YZ3 or :38YZ;style chemicals stick;color identity;select .A:18 or .A:19 or .A:20 or .A:21 or .A:54 or .A:55 or .A:56 or .A:115 or .A:116 or .A:117 or .A:121 or .A:122 or .A:123 or .A:124 or .A:125; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-(aminomethyl)-6-[(2-methyl-3-phenylphenyl)methoxy]-N-(2-phenylethyl)imidazo[1,2-a]pyridin-3-amine | Ligand Info | |||||
| Structure Description | Structure of human Programmed cell death 1 ligand 1 (PD-L1) with inhibitor | PDB:7BEA | ||||
| Method | X-ray diffraction | Resolution | 2.45 Å | Mutation | No | [4] |
| PDB Sequence |
AFTVTVPKDL
27 YVVEYGSNMT37 IECKFPVEKQ47 LDLAALIVYW57 EMEDKNIIQF67 VHGEEDLKVQ 77 HSSYRQRARL87 LKDQLSLGNA97 ALQITDVKLQ107 DAGVYRCMIS117 YGGADYKRIT 127 VKVNAPYAAA137 LEHHHH
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TK2 or .TK22 or .TK23 or :3TK2;style chemicals stick;color identity;select .A:54 or .A:56 or .A:115 or .A:116 or .A:117 or .A:121 or .A:122 or .A:123 or .A:124 or .A:125; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: methyl 3-amino-4-(2-fluorophenyl)-1H-pyrrole-2-carboxylate | Ligand Info | |||||
| Structure Description | PD-L1 IgV domain V76T with fragment | PDB:6NOJ | ||||
| Method | X-ray diffraction | Resolution | 2.33 Å | Mutation | Yes | [2] |
| PDB Sequence |
AFTVTVPKDL
27 YVVEYGSNMT37 IECKFPVEKQ47 LDLAALIVYW57 EMEDKNIIQF67 VHGEEDLKTQ 77 HSSYRQRARL87 LKDQLSLGNA97 ALQITDVKLQ107 DAGVYRCMIS117 YGGADYKRIT 127 VKVNAPYAAA137 LHHHH
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .KW7 or .KW72 or .KW73 or :3KW7;style chemicals stick;color identity;select .A:54 or .A:56 or .A:115 or .A:116 or .A:117 or .A:121 or .A:122 or .A:123; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 1-[5-(3,5-dichlorophenyl)furan-2-yl]-N-methylmethanamine | Ligand Info | |||||
| Structure Description | PD-L1 IgV domain V76T with fragment | PDB:6NOS | ||||
| Method | X-ray diffraction | Resolution | 2.70 Å | Mutation | Yes | [2] |
| PDB Sequence |
AFTVTVPKDL
27 YVVEYGSNMT37 IECKFPVEKQ47 LDLAALIVYW57 EMEDKNIIQF67 VHGEEDLKTQ 77 HSSYRQRARL87 LKDQLSLGNA97 ALQITDVKLQ107 DAGVYRCMIS117 YGGADYKRIT 127 VKVNAPYAAA137 LHHHH
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .KWA or .KWA2 or .KWA3 or :3KWA;style chemicals stick;color identity;select .A:54 or .A:55 or .A:56 or .A:115 or .A:116 or .A:117 or .A:121 or .A:122 or .A:123; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-[[4-[[3-(2,3-Dihydro-1,4-Benzodioxin-6-Yl)-2-Methyl-Phenyl]methoxy]-2,5-Bis(Fluoranyl)phenyl]methylamino]-3-Oxidanylidene-Butanoic Acid | Ligand Info | |||||
| Structure Description | Structure of PD-L1/small-molecule inhibitor complex | PDB:5N2F | ||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | No | [5] |
| PDB Sequence |
> Chain A
AFTVTVPKDL 27 YVVEYGSNMT37 IECKFPVEKQ47 LDLAALIVYW57 EMEDKNIIQF67 VHGEEDLKVQ 77 HSSYRQRARL87 LKDQLSLGNA97 ALQITDVKLQ107 DAGVYRCMIS117 YGGADYKRIT 127 VKVNAPYAAA137 LEHHHH> Chain B AFTVTVPKDL 27 YVVEYGSNMT37 IECKFPVEKQ47 LDLAALIVYW57 EMEDKNIIQF67 VHGEEDLKVQ 77 HSSYRQRARL87 LKDQLSLGNA97 ALQITDVKLQ107 DAGVYRCMIS117 YGGADYKRIT 127 VKVNAPYAAA137 LEHH
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8HW or .8HW2 or .8HW3 or :38HW;style chemicals stick;color identity;select .A:18 or .A:19 or .A:20 or .A:54 or .A:56 or .A:66 or .A:115 or .A:116 or .A:117 or .A:121 or .A:122 or .A:123 or .B:54 or .B:55 or .B:56 or .B:63 or .B:66 or .B:68 or .B:73 or .B:76 or .B:115 or .B:116 or .B:117 or .B:121 or .B:122 or .B:123; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ALA18[A]
4.677
PHE19[A]
2.951
THR20[A]
3.075
ILE54[A]
3.620
TYR56[A]
3.072
GLN66[A]
3.719
MET115[A]
3.699
ILE116[A]
4.035
SER117[A]
4.086
ALA121[A]
3.633
ASP122[A]
3.427
TYR123[A]
3.762
ILE54[B]
3.447
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| Ligand Name: PD-1/PD-L1 inhibitor 17 | Ligand Info | |||||
| Structure Description | Discovery of Novel Small-molecule Inhibitors of PD-1/PD-L1 Axis that Promotes PD-L1 Internalization and Degradation | PDB:7DY7 | ||||
| Method | X-ray diffraction | Resolution | 2.42 Å | Mutation | No | [6] |
| PDB Sequence |
AFTVTVPKDL
27 YVVEYGSNMT37 IECKFPVEKQ47 LDLAALIVYW57 EMEDKNIIQF67 VHGEEDLKVQ 77 HSSYRQRARL87 LKDQLSLGNA97 ALQITDVKLQ107 DAGVYRCMIS117 YGGADYKRIT 127 VKVNAPYAAA137 LEHHHH
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .HOU or .HOU2 or .HOU3 or :3HOU;style chemicals stick;color identity;select .B:54 or .B:55 or .B:56 or .B:58 or .B:63 or .B:66 or .B:76 or .B:115 or .B:116 or .B:117 or .B:121 or .B:122 or .B:123; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (2r)-1-({3-Bromo-4-[(2-Methyl[1,1'-Biphenyl]-3-Yl)methoxy]phenyl}methyl)piperidine-2-Carboxylic Acid | Ligand Info | |||||
| Structure Description | Structure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass inhibitor | PDB:5J8O | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [1] |
| PDB Sequence |
AFTVTVPKDL
27 YVVEYGSNMT37 IECKFPVEKQ47 LDLAALIVYW57 EMEDKNIIQF67 VHGEEDLKVQ 77 HSSYRQRARL87 LKDQLSLGNA97 ALQITDVKLQ107 DAGVYRCMIS117 YGGADYKRIT 127 VKVNAPYAAA137 LE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .6GZ or .6GZ2 or .6GZ3 or :36GZ;style chemicals stick;color identity;select .A:54 or .A:56 or .A:63 or .A:66 or .A:68 or .A:76 or .A:115 or .A:116 or .A:117 or .A:121 or .A:122 or .A:123; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structural basis for small molecule targeting of the programmed death ligand 1 (PD-L1). Oncotarget. 2016 May 24;7(21):30323-35. | ||||
| REF 2 | Fragment-based screening of programmed death ligand 1 (PD-L1). Bioorg Med Chem Lett. 2019 Mar 15;29(6):786-790. | ||||
| REF 3 | Small-molecule inhibitors of PD-1/PD-L1 immune checkpoint alleviate the PD-L1-induced exhaustion of T-cells. Oncotarget. 2017 Aug 7;8(42):72167-72181. | ||||
| REF 4 | Design, Synthesis, and Biological Evaluation of Imidazopyridines as PD-1/PD-L1 Antagonists. ACS Med Chem Lett. 2021 Apr 28;12(5):768-773. | ||||
| REF 5 | 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 Jul 13;60(13):5857-5867. | ||||
| REF 6 | Discovery of Small-Molecule Inhibitors of the PD-1/PD-L1 Axis That Promote PD-L1 Internalization and Degradation. J Med Chem. 2022 Mar 10;65(5):3879-3893. | ||||
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