Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| 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 | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | Nicotinamide-Adenine-Dinucleotide | Ligand Info | |||
| Canonical SMILES | C1=CC(=C[N+](=C1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)N4C=NC5=C(N=CN=C54)N)O)O)O)O)C(=O)N | ||||
| InChI | 1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1 | ||||
| InChIKey | BAWFJGJZGIEFAR-NNYOXOHSSA-N | ||||
| PubChem Compound ID | 5892 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 4WNC Crystal structure of human wild-type GAPDH at 1.99 angstroms resolution | ||||||
| Method | X-ray diffraction | Resolution | 1.99 Å | Mutation | No | [1] |
| 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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|
|
ASN9
2.647
GLY10
2.707
PHE11
3.289
GLY12
2.199
ARG13
2.138
ILE14
1.890
GLY15
3.804
ARG16
3.999
ASN34
2.266
ASP35
2.396
PRO36
2.583
PHE37
2.686
ILE38
2.747
MET46
4.574
GLU79
3.830
ARG80
2.606
ASP81
4.701
PRO82
4.519
ILE85
4.549
GLU97
4.608
|
|||||
| PDB ID: 4WNI Crystal structure of the T229K mutant of human GAPDH at 2.3 angstroems resolution | ||||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | Yes | [1] |
| 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 ELNGKLKGMA232 FRVPTANVSV242 VDLTCRLEKP252 AKYDDIKKVV 262 KQASEGPLKG272 ILGYTEHQVV282 SSDFNSDTHS292 STFDAGAGIA302 LNDHFVKLIS 312 WYDNEFGYSN322 RVVDLMAHMA332 SKE
|
|||||
|
|
ASN9
2.509
GLY10
2.603
PHE11
3.428
GLY12
2.268
ARG13
2.303
ILE14
2.032
GLY15
3.784
ARG16
4.191
ASN34
2.367
ASP35
2.404
PRO36
2.594
PHE37
2.490
ILE38
2.730
MET46
4.613
GLU79
3.755
ARG80
2.467
ASP81
4.595
PRO82
4.222
ILE85
4.525
GLU97
4.642
|
|||||
| PDB ID: 6ADE Crystal structure of phosphorylated mutant of glyceraldehyde 3-phosphate dehydrogenase from human placenta at 3.15A resolution | ||||||
| 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
|
|||||
|
|
ASN9
3.368
GLY10
3.698
PHE11
3.633
GLY12
3.080
ARG13
3.029
ILE14
3.107
GLY15
4.352
ARG16
4.671
ASN34
3.648
ASP35
2.949
PRO36
3.202
PHE37
3.387
ILE38
3.694
GLU79
3.905
ARG80
3.276
|
|||||
| PDB ID: 6M61 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) with inhibitor heptelidic acid | ||||||
| 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 #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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
|
|||||
| PDB ID: 3GPD TWINNING IN CRYSTALS OF HUMAN SKELETAL MUSCLE D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE | ||||||
| Method | X-ray diffraction | Resolution | 3.50 Å | Mutation | No | [4] |
| PDB Sequence |
GKVKVGVDGF
10 GRIGRLVTRA20 AFNSGKVDIV30 AINDPFIDLH40 YMVYMFQYDS50 THGKFHGTVK 60 AEDGKLVIDG70 KAITIFQERD80 PENIKWGDAG90 TAYVVESTGV100 FTTMEKAGAH 110 LKGGAKRIVI120 SAPSADAPMF130 VMGVNHFKYA140 NSLKIISNAS150 CTTNCLAPLA 160 KVIHDHFGIV170 EGLMTTVHAI180 TATQKTVDSP190 SGKLWRGGRG200 AAQNLIPAST 210 GAAKAVGKVI220 PELDGKLTGM230 AFRVPTANVS240 VLDLTCRLEK250 PAKYDDIKKV 260 VKEASEGPLK270 GILGYTEDEV280 VSDDFNGSNH290 SSIFDAGAGI300 ELNDTFVKLV 310 SWYDNEFGYS320 ERVVDLMAHM330 ASKE
|
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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 .R:8 or .R:9 or .R:10 or .R:11 or .R:12 or .R:13 or .R:14 or .R:33 or .R:34 or .R:35 or .R:36 or .R:77 or .R:78 or .R:79 or .R:80 or .R:81 or .R:97 or .R:98 or .R:99 or .R:101 or .R:121 or .R:122 or .R:123 or .R:151 or .R:180 or .R:181 or .R:182 or .R:315 or .R:316 or .R:319; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ASP8
3.982
GLY9
3.545
PHE10
4.555
GLY11
2.985
ARG12
2.360
ILE13
2.650
GLY14
4.414
ASN33
3.351
ASP34
3.500
PRO35
3.193
PHE36
3.401
GLN77
4.434
GLU78
2.804
ARG79
3.974
ASP80
3.610
|
|||||
| PDB ID: 1ZNQ Crystal Structure of Human Liver GAPDH | ||||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | No | [5] |
| 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
|
|||||
|
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: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:103 or .O:122 or .O:123 or .O:151 or .O:152 or .O:182 or .O:183 or .O:316 or .O:317 or .O:320; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ASN9
3.422
GLY10
3.362
PHE11
3.552
GLY12
2.835
ARG13
2.848
ILE14
2.890
GLY15
4.468
ASN34
3.630
ASP35
2.942
PRO36
3.449
PHE37
3.404
ILE38
3.399
GLU79
3.864
ARG80
3.093
SER98
3.545
|
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | A dimer interface mutation in glyceraldehyde-3-phosphate dehydrogenase regulates its binding to AU-rich RNA. J Biol Chem. 2015 Jan 16;290(3):1770-85. | ||||
| 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 | Twinning in crystals of human skeletal muscle D-glyceraldehyde-3-phosphate dehydrogenase. J Mol Biol. 1976 Jun 14;104(1):277-83. | ||||
| REF 5 | Crystal Structure Analysis of Human liver GAPDH | ||||
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