Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T07400 | Target Info | |||
| Target Name | Advanced glycosylation end product receptor (AGER) | ||||
| Synonyms | Receptor foradvanced glycosylation end products; RAGESEC; RAGE; AGER | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | AGER | ||||
| Biochemical Class | Immunoglobulin | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: 3-[3-({[3-(4-carboxyphenoxy)phenyl]methoxy}methyl)phenyl]-1H-indole-2-carboxylic acid | Ligand Info | |||||
| Structure Description | Receptor for Advanced Glycation End Products VC1 domain in complex with 3-(3-((4-(4-carboxyphenoxy)benzyl)oxy)phenyl)-1H-indole-2-carboxylic acid | PDB:6XQ1 | ||||
| Method | X-ray diffraction | Resolution | 1.51 Å | Mutation | No | [1] |
| PDB Sequence |
GAMAQNITAR
29 IGEPLVLKCK39 GAPKKPPQRL49 EWKLNTGRTE59 AWKVLSPQGG69 GPWDSVARVL 79 PNGSLFLPAV89 GIQDEGIFRC99 QAMNRNGKET109 KSNYRVRVYQ119 IPGKPEIVDS 129 ASELTAGVPN139 KVGTCVSEGS149 YPAGTLSWHL159 DGKPLVPNEK169 GVSVKEQTRR 179 HPETGLFTLQ189 SELMVTPARG199 GDPRPTFSCS209 FSPGLPRHRA219 LRTAPIQPRV 229 WE
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| Ligand Name: 3-(3-{[3-(4-carboxyphenoxy)phenyl]methoxy}phenyl)-1H-indole-2-carboxylic acid | Ligand Info | |||||
| Structure Description | Receptor for Advanced Glycation End Products VC1 domain in complex with 3-(3-(((3-(4-Carboxyphenoxy)benzyl)oxy)methyl)phenyl)-1H-indole-2-carboxylic acid | PDB:6XQ3 | ||||
| Method | X-ray diffraction | Resolution | 1.71 Å | Mutation | No | [1] |
| PDB Sequence |
GAMAQNITAR
29 IGEPLVLKCK39 GAPKKPPQRL49 EWKLNTGRTE59 AWKVLSPQGG69 GPWDSVARVL 79 PNGSLFLPAV89 GIQDEGIFRC99 QAMNRNGKET109 KSNYRVRVYQ119 IPGKPEIVDS 129 ASELTAGVPN139 KVGTCVSEGS149 YPAGTLSWHL159 DGKPLVPNEK169 GVSVKEQTRR 179 HPETGLFTLQ189 SELMVTPARG199 GDPRPTFSCS209 FSPGLPRHRA219 LRTAPIQPRV 229 WE
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ALA21
3.466
MET22
2.781
ALA23
3.907
GLN24
4.276
LYS39
3.023
PRO45
2.687
GLN47
4.450
GLU50
3.197
TRP51
4.253
LYS52
3.317
PRO66
3.169
GLN67
3.220
ASP73
2.701
SER74
3.077
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| Ligand Name: 5-bromo-3-methyl-1H-indole-2-carboxylic Acid | Ligand Info | |||||
| Structure Description | Receptor for Advanced Glycation End Products VC1 domain in complex with Fragment 5 | PDB:6XQ7 | ||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [1] |
| PDB Sequence |
GAMAQNITAR
29 IGEPLVLKCK39 GAPKKPPQRL49 EWKLNTGRTE59 AWKVLSPQGG69 GPWDSVARVL 79 PNGSLFLPAV89 GIQDEGIFRC99 QAMNRNGKET109 KSNYRVRVYQ119 IPGKPEIVDS 129 ASELTAGVPN139 KVGTCVSEGS149 YPAGTLSWHL159 DGKPLVPNEK169 GVSVKEQTRR 179 HPETGLFTLQ189 SELMVTPARG199 GDPRPTFSCS209 FSPGLPRHRA219 LRTAPIQPRV 229 WE
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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 .V6V or .V6V2 or .V6V3 or :3V6V;style chemicals stick;color identity;select .A:48 or .A:49 or .A:50 or .A:77 or .A:78 or .A:79 or .A:80 or .A:85 or .A:100 or .A:101 or .A:102 or .A:108; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 7-methyl-3-phenyl-1H-indole-2-carboxylic acid | Ligand Info | |||||
| Structure Description | Receptor for Advanced Glycation End Products VC1 domain in complex with Fragment 1 | PDB:6XQ5 | ||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [1] |
| PDB Sequence |
GAMAQNITAR
29 IGEPLVLKCK39 GAPKKPPQRL49 EWKLNTGRTE59 AWKVLSPQGG69 GPWDSVARVL 79 PNGSLFLPAV89 GIQDEGIFRC99 QAMNRNGKET109 KSNYRVRVYQ119 IPGKPEIVDS 129 ASELTAGVPN139 KVGTCVSEGS149 YPAGTLSWHL159 DGKPLVPNEK169 GVSVKEQTRR 179 HPETGLFTLQ189 SELMVTPARG199 GDPRPTFSCS209 FSPGLPRHRA219 LRTAPIQPRV 229 WE
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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 .V6M or .V6M2 or .V6M3 or :3V6M;style chemicals stick;color identity;select .A:21 or .A:50 or .A:51 or .A:52 or .A:98 or .A:99 or .A:100 or .A:110 or .A:111 or .A:112; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 3-Phenoxyphenol | Ligand Info | |||||
| Structure Description | Receptor for Advanced Glycation End Products VC1 domain in complex with Fragments 1 & 11 | PDB:6XQ8 | ||||
| Method | X-ray diffraction | Resolution | 1.82 Å | Mutation | No | [1] |
| PDB Sequence |
GAMAQNITAR
29 IGEPLVLKCK39 GAPKKPPQRL49 EWKLNTGRTE59 AWKVLSPQGG69 GPWDSVARVL 79 PNGSLFLPAV89 GIQDEGIFRC99 QAMNRNGKET109 KSNYRVRVYQ119 IPGKPEIVDS 129 ASELTAGVPN139 KVGTCVSEGS149 YPAGTLSWHL159 DGKPLVPNEK169 GVSVKEQTRR 179 HPETGLFTLQ189 SELMVTPARG199 GDPRPTFSCS209 FSPLRTAPIQ226 PRVWE |
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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 .V6P or .V6P2 or .V6P3 or :3V6P;style chemicals stick;color identity;select .A:47 or .A:48 or .A:49 or .A:50 or .A:63 or .A:64 or .A:65 or .A:66 or .A:73 or .A:74 or .A:75 or .A:76 or .A:77 or .A:85 or .A:87 or .A:100 or .A:101; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 6-iodo-1H-indole-2-carboxylic Acid | Ligand Info | |||||
| Structure Description | Receptor for Advanced Glycation End Products VC1 domain in complex with 3-(3-(((3-(4-Carboxyphenoxy)benzyl)oxy)methyl)phenyl)-1H-indole-2-carboxylic acid | PDB:7LML | ||||
| Method | X-ray diffraction | Resolution | 2.15 Å | Mutation | No | [1] |
| PDB Sequence |
GAMAQNITAR
29 IGEPLVLKCK39 GAPKKPPQRL49 EWKLNTGRTE59 AWKVLSPQGG69 GPWDSVARVL 79 PNGSLFLPAV89 GIQDEGIFRC99 QAMNRNGKET109 KSNYRVRVYQ119 IPGKPEIVDS 129 ASELTAGVPN139 KVGTCVSEGS149 YPAGTLSWHL159 DGKPLVPNEK169 GVSVKEQTRR 179 HPETGLFTLQ189 SELMVTPARG199 GDPRPTFSCS209 FSPGLPRHRA219 LRTAPIQPRV 229 WE
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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 .Y6S or .Y6S2 or .Y6S3 or :3Y6S;style chemicals stick;color identity;select .A:21 or .A:22 or .A:47 or .A:48 or .A:49 or .A:50 or .A:51 or .A:52 or .A:73 or .A:74 or .A:75 or .A:77 or .A:78 or .A:79 or .A:80 or .A:85 or .A:87 or .A:98 or .A:99 or .A:100 or .A:101 or .A:102 or .A:108 or .A:110 or .A:111 or .A:112; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ALA21
4.505
MET22
4.838
GLN47
4.839
ARG48
3.317
LEU49
3.500
GLU50
2.681
TRP51
3.723
LYS52
3.097
ASP73
3.365
SER74
3.118
VAL75
4.281
ARG77
3.243
VAL78
3.201
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| Ligand Name: 4-(3-Hydroxyphenoxy)benzoic acid | Ligand Info | |||||
| Structure Description | Receptor for Advanced Glycation End Products VC1 domain in complex with Fragments 1 & 13 | PDB:6XQ9 | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [1] |
| PDB Sequence |
GAMAQNITAR
29 IGEPLVLKCK39 GAPKKPPQRL49 EWKLNTGRTE59 AWKVLSPQGG69 GPWDSVARVL 79 PNGSLFLPAV89 GIQDEGIFRC99 QAMNRNGKET109 KSNYRVRVYQ119 IPGKPEIVDS 129 ASELTAGVPN139 KVGTCVSEGS149 YPAGTLSWHL159 DGKPLVPNEK169 GVSVKEQTRR 179 HPETGLFTLQ189 SELMVTPARG199 GDPRPTFSCS209 FSPGLPRHRA219 LRTAPIQPRV 229 WE
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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 .V6S or .V6S2 or .V6S3 or :3V6S;style chemicals stick;color identity;select .A:47 or .A:48 or .A:49 or .A:50 or .A:73 or .A:74 or .A:77 or .A:78 or .A:79 or .A:80 or .A:85 or .A:87 or .A:100 or .A:101 or .A:102 or .A:108; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 7-methyl-3-(1~{H}-pyrazol-4-yl)-1~{H}-indole-2-carboxylic acid | Ligand Info | |||||
| Structure Description | Receptor for Advanced Glycation End Products VC1 domain in complex with 3-(3-((4-(4-carboxyphenoxy)benzyl)oxy)phenyl)-1H-indole-2-carboxylic acid | PDB:7LMW | ||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | No | [1] |
| PDB Sequence |
GAMAQNITAR
29 IGEPLVLKCK39 GAPKKPPQRL49 EWKLNTGRTE59 AWKVLSPQGG69 GPWDSVARVL 79 PNGSLFLPAV89 GIQDEGIFRC99 QAMNRNGKET109 KSNYRVRVYQ119 IPGKPEIVDS 129 ASELTAGVPN139 KVGTCVSEGS149 YPAGTLSWHL159 DGKPLVPNEK169 GVSVKEQTRR 179 HPETGLFTLQ189 SELMVTPARG199 GDPRPTFSCS209 FSPHRALRTA223 PIQPRVWE |
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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 .Y6P or .Y6P2 or .Y6P3 or :3Y6P;style chemicals stick;color identity;select .A:21 or .A:50 or .A:51 or .A:52 or .A:62 or .A:69 or .A:70 or .A:71 or .A:72 or .A:98 or .A:99 or .A:100 or .A:110 or .A:111 or .A:112; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: N~5~-[(5r)-5-Methyl-4-Oxo-4,5-Dihydro-1h-Imidazol-2-Yl]-L-Ornithine | Ligand Info | |||||
| Structure Description | Receptor for Advanced Glycation End Products (RAGE) Specifically Recognizes Methylglyoxal Derived AGEs. | PDB:2MOV | ||||
| Method | Solution NMR | Resolution | N.A. | Mutation | No | [2] |
| PDB Sequence |
GSAQNITARI
10 GEPLVLKCKG20 APKKPPQRLE30 WKLNTGRTEA40 WKVLSPQGGG50 PWDSVARVLP 60 NGSLFLPAVG70 IQDEGIFRCQ80 AMNRNGKETK90 SNYRVRVYQI100 PGKPE |
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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 .IOR or .IOR2 or .IOR3 or :3IOR;style chemicals stick;color identity;select .A:2 or .A:3 or .A:30 or .A:31 or .A:32 or .A:76 or .A:77 or .A:78 or .A:79 or .A:80 or .A:81 or .A:89 or .A:90 or .A:91 or .A:92; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: N-(4-{7-cyano-4-[(morpholin-4-yl)methyl]quinolin-2-yl}phenyl)acetamide | Ligand Info | |||||
| Structure Description | Structure of the C-terminal Domain of RAGE and Its Inhibitor | PDB:6VXG | ||||
| Method | Solution NMR | Resolution | N.A. | Mutation | No | [3] |
| PDB Sequence |
MWQRRQRRGE
10 ERKAPE
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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 .RQV or .RQV2 or .RQV3 or :3RQV;style chemicals stick;color identity;select .A:1 or .A:2 or .A:4 or .A:5 or .A:8 or .A:10 or .A:12 or .A:13 or .A:14 or .A:15 or .A:16; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | A fragment-based approach to discovery of Receptor for Advanced Glycation End products inhibitors. Proteins. 2021 Nov;89(11):1399-1412. | ||||
| REF 2 | The receptor for advanced glycation end products (RAGE) specifically recognizes methylglyoxal-derived AGEs. Biochemistry. 2014 May 27;53(20):3327-35. | ||||
| REF 3 | Small-molecule antagonism of the interaction of the RAGE cytoplasmic domain with DIAPH1 reduces diabetic complications in mice. Sci Transl Med. 2021 Nov 24;13(621):eabf7084. | ||||
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