Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T77721 | Target Info | |||
| Target Name | Glycerol-3-phosphate dehydrogenase (GPD1) | ||||
| Synonyms | Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic; GPDH-C; GPD-C | ||||
| Target Type | Literature-reported Target | ||||
| Gene Name | GPD1 | ||||
| Biochemical Class | Short-chain dehydrogenases reductase | ||||
| 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: 6PYP Binary Complex of Human Glycerol 3-Phosphate Dehydrogenase, R269A mutant | ||||||
| Method | X-ray diffraction | Resolution | 1.95 Å | Mutation | Yes | [1] |
| PDB Sequence |
ASKKVCIVGS
11 GNWGSAIAKI21 VGGNAAQLAQ31 FDPRVTMWVF41 EEDIGGKKLT51 EIINTQHENV 61 KYLPGHKLPP71 NVVAVPDVVQ81 AAEDADILIF91 VVPHQFIGKI101 CDQLKGHLKA 111 NATGISLIKG121 VDEGPNGLKL131 ISEVIGERLG141 IPMSVLMGAN151 IASEVADEKF 161 CETTIGCKDP171 AQGQLLKELM181 QTPNFRITVV191 QEVDTVEICG201 ALKNVVAVGA 211 GFCDGLGFGD221 NTKAAVIRLG231 LMEMIAFAKL241 FCSGPVSSAT251 FLESCGVADL 261 ITTCYGGANR271 KVAEAFARTG281 KSIEQLEKEL291 LNGQKLQGPE301 TARELYSILQ 311 HKGLVDKFPL321 FMAVYKVCYE331 GQPVGEFIHC341 LQNHPEHM
|
|||||
|
|
GLY10
3.089
SER11
2.680
GLY12
2.538
ASN13
2.165
TRP14
2.260
GLY15
3.214
TRP39
3.000
VAL40
4.203
PHE41
2.442
GLU43
4.021
ASN60
4.604
TYR63
2.946
VAL92
3.266
|
|||||
| PDB ID: 6E90 Ternary complex of human glycerol 3-phosphate dehydrogenase | ||||||
| Method | X-ray diffraction | Resolution | 2.05 Å | Mutation | No | [2] |
| PDB Sequence |
ASKKVCIVGS
11 GNWGSAIAKI21 VGGNAAQLAQ31 FDPRVTMWVF41 EEDIGGKKLT51 EIINTQHENV 61 KYLPGHKLPP71 NVVAVPDVVQ81 AAEDADILIF91 VVPHQFIGKI101 CDQLKGHLKA 111 NATGISLIKG121 VDEGPNGLKL131 ISEVIGERLG141 IPMSVLMGAN151 IASEVADEKF 161 CETTIGCKDP171 AQGQLLKELM181 QTPNFRITVV191 QEVDTVEICG201 ALKNVVAVGA 211 GFCDGLGFGD221 NTKAAVIRLG231 LMEMIAFAKL241 FCSSATFLES255 CGVADLITTC 265 YGGRNRKVAE275 AFARTGKSIE285 QLEKELLNGQ295 KLQGPETARE305 LYSILQHKGL 315 VDKFPLFMAV325 YKVCYEGQPV335 GEFIHCLQNH345 PEHM
|
|||||
|
|
GLY10
4.830
SER11
2.637
GLY12
2.689
ASN13
2.056
TRP14
2.061
GLY15
2.207
SER16
4.821
TRP39
2.482
VAL40
4.418
PHE41
2.219
GLU43
3.733
LEU50
4.903
ASN60
4.780
TYR63
2.527
VAL92
2.667
VAL93
2.713
PRO94
2.625
HIS95
3.285
PHE97
3.014
|
|||||
| PDB ID: 6E8Z Binary complex of Human glycerol 3-phosphate dehydrogenase with NAD | ||||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [2] |
| PDB Sequence |
ASKKVCIVGS
11 GNWGSAIAKI21 VGGNAAQLAQ31 FDPRVTMWVF41 EEDIKKLTEI53 INTQHENVKY 63 LPGHKLPPNV73 VAVPDVVQAA83 EDADILIFVV93 PHQFIGKICD103 QLKGHLKANA 113 TGISLIKGLK130 LISEVIGERL140 GIPMSVLMGA150 NIASEVADEK160 FCETTIGCKD 170 PAQGQLLKEL180 MQTPNFRITV190 VQEVDTVEIC200 GALKNVVAVG210 AGFCDGLGFG 220 DNTKAAVIRL230 GLMEMIAFAK240 LFCSGPVSSA250 TFLESCGVAD260 LITTCYGGRN 270 RKVAEAFART280 GKSIEQLEKE290 LLGQKLQGPE301 TARELYSILQ311 HKGLVDKFPL 321 FMAVYKVCYE331 GQPVGEFIHC341 LQNHPEHM
|
|||||
|
|
GLY10
2.934
SER11
2.496
GLY12
2.201
ASN13
2.087
TRP14
2.012
GLY15
3.226
TRP39
2.126
VAL40
4.844
PHE41
2.621
GLU43
4.401
ASN60
4.632
TYR63
3.236
VAL92
2.858
VAL93
2.720
|
|||||
| PDB ID: 1WPQ Ternary Complex Of Glycerol 3-phosphate Dehydrogenase 1 with NAD and dihydroxyactone | ||||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | No | [3] |
| PDB Sequence |
ASKKVCIVGS
11 GNWGSAIAKI21 VGGNAAQLAQ31 FDPRVTMWVF41 EEDIGGKKLT51 EIINTQHENV 61 KYLPGHKLPP71 NVVAVPDVVQ81 AAEDADILIF91 VVPHQFIGKI101 CDQLKGHLKA 111 NPTGISLIKG121 VDEGPNGLKL131 ISEVIGERLG141 IPMSVLMGAN151 IASEVADEKF 161 CETTIGCKDP171 AQGQLLKELM181 QTPNFRITVV191 QEVDTVEICG201 ALKNVVAVGA 211 GFCDGLGFGD221 NTKAAVIRLG231 LMEMIAFAKL241 FCSGPVSSAT251 FLESCGVADL 261 ITTCYGGRNR271 KVAEAFARTG281 KSIEQLEKEL291 LNGQKLQGPE301 TARELYSILQ 311 HKGLVDKFPL321 FMAVYKVCYE331 GQPVGEFIHC341 LQNHPEHM
|
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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 .A:11 or .A:12 or .A:13 or .A:14 or .A:15 or .A:39 or .A:41 or .A:43 or .A:63 or .A:92 or .A:93 or .A:94 or .A:95 or .A:97 or .A:101 or .A:118 or .A:119 or .A:120 or .A:151 or .A:152 or .A:153 or .A:205 or .A:269 or .A:294 or .A:295 or .A:296 or .A:298; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
SER11
3.554
GLY12
3.162
ASN13
2.723
TRP14
3.152
GLY15
3.111
TRP39
3.735
PHE41
3.516
GLU43
3.740
TYR63
3.620
VAL92
3.657
VAL93
3.819
PRO94
3.272
HIS95
4.132
PHE97
3.357
|
|||||
| PDB ID: 1X0X Co-Structure of Homo Sapiens Glycerol-3-Phosphate Dehydrogenase 1 complex with NAD | ||||||
| Method | X-ray diffraction | Resolution | 2.75 Å | Mutation | No | [3] |
| PDB Sequence |
SMASKKVCIV
9 GSGNWGSAIA19 KIVGGNAAQL29 AQFDPRVTMW39 VFEEDIGGKK49 LTEIINTQHE 59 NVKYLPGHKL69 PPNVVAVPDV79 VQAAEDADIL89 IFVVPHQFIG99 KICDQLKGHL 109 KANATGISLI119 KGVDEGPNGL129 KLISEVIGER139 LGIPMSVLMG149 ANIASEVADE 159 KFCETTIGCK169 DPAQGQLLKE179 LMQTPNFRIT189 VVQEVDTVEI199 CGALKNVVAV 209 GAGFCDGLGF219 GDNTKAAVIR229 LGLMEMIAFA239 KLFCSGPVSS249 ATFLESCGVA 259 DLITTCYGGR269 NRKVAEAFAR279 TGKSIEQLEK289 ELLNGQKLQG299 PETARELYSI 309 LQHKGLVDKF319 PLFMAVYKVC329 YEGQPVGEFI339 HCLQNHPEHM349 |
|||||
|
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 .A:11 or .A:12 or .A:13 or .A:14 or .A:15 or .A:39 or .A:41 or .A:43 or .A:63 or .A:92 or .A:93 or .A:94 or .A:95 or .A:97 or .A:118 or .A:119 or .A:120 or .A:149 or .A:151 or .A:152 or .A:153 or .A:205 or .A:269 or .A:294 or .A:295 or .A:296 or .A:298; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
SER11
3.678
GLY12
2.933
ASN13
2.772
TRP14
2.949
GLY15
2.920
TRP39
3.747
PHE41
3.406
GLU43
4.606
TYR63
3.479
VAL92
3.722
VAL93
3.660
PRO94
3.462
HIS95
4.567
PHE97
3.398
|
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Modeling the Role of a Flexible Loop and Active Site Side Chains in Hydride Transfer Catalyzed by Glycerol-3-phosphate Dehydrogenase. ACS Catal. 2020 Oct 2;10(19):11253-11267. | ||||
| REF 2 | Human Glycerol 3-Phosphate Dehydrogenase: X-ray Crystal Structures That Guide the Interpretation of Mutagenesis Studies. Biochemistry. 2019 Feb 26;58(8):1061-1073. | ||||
| REF 3 | Crystal structures of human glycerol 3-phosphate dehydrogenase 1 (GPD1). J Mol Biol. 2006 Mar 31;357(3):858-69. | ||||
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