Binding Site Information of Target
| Target General Information | Top | ||||
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| Target ID | T39321 | Target Info | |||
| Target Name | Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) | ||||
| Synonyms | Peptidyl-cysteine S-nitrosylase GAPDH; OK/SW-cl.12; GAPD; D-glyceraldehyde-3-phosphate dehydrogenase; CDABP0047 | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | GAPDH | ||||
| Biochemical Class | Aldehyde/oxo donor oxidoreductase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: S-sulpho-L-cysteine | Ligand Info | |||||
| Structure Description | GAPDH purified from the supernatant of HEK293F cells: crystal form 1 of 4. | PDB:6YND | ||||
| Method | X-ray diffraction | Resolution | 1.52 Å | Mutation | No | [1] |
| PDB Sequence |
GKVKVGVNGF
11 GRIGRLVTRA21 AFNSGKVDIV31 AINDPFIDLN41 YMVYMFQYDS51 THGKFHGTVK 61 AENGKLVING71 NPITIFQERD81 PSKIKWGDAG91 AEYVVESTGV101 FTTMEKAGAH 111 LQGGAKRVII121 SAPSADAPMF131 VMGVNHEKYD141 NSLKIISNAS151 TTNCLAPLAK 162 VIHDNFGIVE172 GLMTTVHAIT182 ATQKTVDGPS192 GKLWRDGRGA202 LQNIIPASTG 212 AAKAVGKVIP222 ELNGKLTGMA232 FRVPTANVSV242 VDLTCRLEKP252 AKYDDIKKVV 262 KQASEGPLKG272 ILGYTEHQVV282 SSDFNSDTHS292 STFDAGAGIA302 LNDHFVKLIS 312 WYDNEFGYSN322 RVVDLMAHMA332 SKE
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: L-serine-O-phosphate | Ligand Info | |||||
| Structure Description | Crystal structure of phosphorylated mutant of glyceraldehyde 3-phosphate dehydrogenase from human placenta at 3.15A resolution | PDB:6ADE | ||||
| Method | X-ray diffraction | Resolution | 3.15 Å | Mutation | Yes | [2] |
| PDB Sequence |
KVKVGVNGFG
12 RIGRLVTRAA22 FNSGKVDIVA32 INDPFIDLNY42 MVYMFQYDTH53 GKFHGTVKAE 63 NGKLVINGNP73 ITIFQERDPS83 KIKWGDAGAE93 YVVESTGVFT103 TMEKAGAHLQ 113 GGAKRVIISA123 PSADAPMFVM133 GVNHEKYDNS143 LKIISNACTT154 NCLAPLAKVI 164 HDNFGIVEGL174 MTTVHAITAT184 QKTVDGPSGK194 LWRDGRGALQ204 NIIPASTGAA 214 KAVGKVIPEL224 NGKLTGMAFR234 VPTANVSVVD244 LTCRLEKPAK254 YDDIKKVVKQ 264 ASEGPLLGIL274 GYTEHQVVSS284 DFNSDTHSST294 FDAGAGIALN304 DHFVKLISWY 314 DNEFGYSNRV324 VDLMAHMASK334 E
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| Ligand Name: Nicotinamide-Adenine-Dinucleotide | Ligand Info | |||||
| Structure Description | Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) with inhibitor heptelidic acid | PDB:6M61 | ||||
| Method | X-ray diffraction | Resolution | 1.82 Å | Mutation | No | [3] |
| PDB Sequence |
FMGKVKVGVN
9 GFGRIGRLVT19 RAAFNSGKVD29 IVAINDPFID39 LNYMVYMFQY49 DSTHGKFHGT 59 VKAENGKLVI69 NGNPITIFQE79 RDPSKIKWGD89 AGAEYVVEST99 GVFTTMEKAG 109 AHLQGGAKRV119 IISAPSADAP129 MFVMGVNHEK139 YDNSLKIISN149 ASCTTNCLAP 159 LAKVIHDNFG169 IVEGLMTTVH179 AITATQKTVD189 GPSGKLWRDG199 RGALQNIIPA 209 STGAAKAVGK219 VIPELNGKLT229 GMAFRVPTAN239 VSVVDLTCRL249 EKPAKYDDIK 259 KVVKQASEGP269 LKGILGYTEH279 QVVSSDFNSD289 THSSTFDAGA299 GIALNDHFVK 309 LISWYDNEFG319 YSNRVVDLMA329 HMASKE
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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 .NAD or .NAD2 or .NAD3 or :3NAD;style chemicals stick;color identity;select .O:9 or .O:10 or .O:11 or .O:12 or .O:13 or .O:14 or .O:15 or .O:16 or .O:34 or .O:35 or .O:36 or .O:37 or .O:38 or .O:79 or .O:80 or .O:98 or .O:99 or .O:100 or .O:101 or .O:102 or .O:122 or .O:123 or .O:151 or .O:152 or .O:179 or .O:182 or .O:183 or .O:316 or .O:317 or .O:320; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ASN9
3.310
GLY10
3.513
PHE11
3.662
GLY12
3.159
ARG13
3.011
ILE14
2.788
GLY15
4.455
ARG16
4.929
ASN34
3.545
ASP35
2.842
PRO36
3.298
PHE37
3.544
ILE38
3.714
GLU79
3.703
ARG80
3.122
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 3,6,9,12,15,18,21,24,27-Nonaoxanonacosane-1,29-diol | Ligand Info | |||||
| Structure Description | GAPDH purified from the supernatant of HEK293F cells: crystal form 1 of 4. | PDB:6YND | ||||
| Method | X-ray diffraction | Resolution | 1.52 Å | Mutation | No | [1] |
| PDB Sequence |
GKVKVGVNGF
11 GRIGRLVTRA21 AFNSGKVDIV31 AINDPFIDLN41 YMVYMFQYDS51 THGKFHGTVK 61 AENGKLVING71 NPITIFQERD81 PSKIKWGDAG91 AEYVVESTGV101 FTTMEKAGAH 111 LQGGAKRVII121 SAPSADAPMF131 VMGVNHEKYD141 NSLKIISNAS151 TTNCLAPLAK 162 VIHDNFGIVE172 GLMTTVHAIT182 ATQKTVDGPS192 GKLWRDGRGA202 LQNIIPASTG 212 AAKAVGKVIP222 ELNGKLTGMA232 FRVPTANVSV242 VDLTCRLEKP252 AKYDDIKKVV 262 KQASEGPLKG272 ILGYTEHQVV282 SSDFNSDTHS292 STFDAGAGIA302 LNDHFVKLIS 312 WYDNEFGYSN322 RVVDLMAHMA332 SKE
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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 .XPE or .XPE2 or .XPE3 or :3XPE;style chemicals stick;color identity;select .A:127 or .A:128 or .A:129 or .A:130 or .A:131 or .A:136 or .A:139 or .A:140 or .A:141 or .A:144 or .A:219 or .A:220 or .A:222; 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: Monomethyl maleate | Ligand Info | |||||
| Structure Description | Crystal structure of GAPDH | PDB:6IQ6 | ||||
| Method | X-ray diffraction | Resolution | 2.29 Å | Mutation | No | [4] |
| PDB Sequence |
KVKVGVNGFG
12 RIGRLVTRAA22 FNSGKVDIVA32 INDPFIDLNY42 MVYMFQYDST52 HGKFHGTVKA 62 ENGKLVINGN72 PITIFQERDP82 SKIKWGDAGA92 EYVVESTGVF102 TTMEKAGAHL 112 QGGAKRVIIS122 APSADAPMFV132 MGVNHEKYDN142 SLKIISNASC152 TTNCLAPLAK 162 VIHDNFGIVE172 GLMTTVHAIT182 ATQKTVDGPS192 GKLWRDGRGA202 LQNIIPASTG 212 AAKAVGKVIP222 ELNGKLTGMA232 FRVPTANVSV242 VDLTCRLEKP252 AKYDDIKKVV 262 KQASEGPLKG272 ILGYTEHQVV282 SSDFNSDTHS292 STFDAGAGIA302 LNDHFVKLIS 312 WYDNEFGYSN322 RVVDLMAHMA332 SKE
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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 .AW9 or .AW92 or .AW93 or :3AW9;style chemicals stick;color identity;select .A:13 or .A:14 or .A:122 or .A:151 or .A:152 or .A:153 or .A:179 or .A:182 or .A:316 or .A:317 or .A:320; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (5aS,6R,9S,9aS)-9-hydroxy-9-methyl-1-oxo-6-propan-2-yl-3,5a,6,7,8,9a-hexahydro-2-benzoxepine-4-carboxylic acid | Ligand Info | |||||
| Structure Description | Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) with inhibitor heptelidic acid | PDB:6M61 | ||||
| Method | X-ray diffraction | Resolution | 1.82 Å | Mutation | No | [3] |
| PDB Sequence |
FMGKVKVGVN
9 GFGRIGRLVT19 RAAFNSGKVD29 IVAINDPFID39 LNYMVYMFQY49 DSTHGKFHGT 59 VKAENGKLVI69 NGNPITIFQE79 RDPSKIKWGD89 AGAEYVVEST99 GVFTTMEKAG 109 AHLQGGAKRV119 IISAPSADAP129 MFVMGVNHEK139 YDNSLKIISN149 ASCTTNCLAP 159 LAKVIHDNFG169 IVEGLMTTVH179 AITATQKTVD189 GPSGKLWRDG199 RGALQNIIPA 209 STGAAKAVGK219 VIPELNGKLT229 GMAFRVPTAN239 VSVVDLTCRL249 EKPAKYDDIK 259 KVVKQASEGP269 LKGILGYTEH279 QVVSSDFNSD289 THSSTFDAGA299 GIALNDHFVK 309 LISWYDNEFG319 YSNRVVDLMA329 HMASKE
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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 .F4F or .F4F2 or .F4F3 or :3F4F;style chemicals stick;color identity;select .O:123 or .O:124 or .O:150 or .O:151 or .O:152 or .O:153 or .O:177 or .O:179 or .O:182 or .O:209 or .O:210 or .O:211 or .O:212 or .O:213 or .O:232 or .O:234 or .O:314 or .O:316; 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 | Partial catalytic Cys oxidation of human GAPDH to Cys-sulfonic acid. Wellcome Open Res. 2020 Aug 25;5:114. | ||||
| REF 2 | Crystal structure of phosphorylated mutant of glyceraldehyde 3-phosphate dehydrogenase from human placenta at 3.15A resolution | ||||
| REF 3 | Biosynthesis of the fungal glyceraldehyde-3-phosphate dehydrogenase inhibitor heptelidic acid and mechanism of self-resistance. doi:10.1039/D0SC03805A. | ||||
| REF 4 | Structural Study of Monomethyl Fumarate-Bound Human GAPDH. Mol Cells. 2019 Aug 31;42(8):597-603. | ||||
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