Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T12646 | Target Info | |||
| Target Name | Valosin-containing protein p97 (VCP) | ||||
| Synonyms | Valosin-containing protein; Transitional endoplasmic reticulum ATPase; TER ATPase; 15S Mg(2+)-ATPase p97 subunit | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | VCP | ||||
| Biochemical Class | Acid anhydride hydrolase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | AMP-PNP | Ligand Info | |||
| Canonical SMILES | C1=NC(=C2C(=N1)N(C=N2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N | ||||
| InChI | 1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1 | ||||
| InChIKey | PVKSNHVPLWYQGJ-KQYNXXCUSA-N | ||||
| PubChem Compound ID | 33113 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 7BPA Human AAA+ ATPase VCP mutant - T76A, AMP-PNP-bound form, Conformation I | ||||||
| Method | Electron microscopy | Resolution | 3.30 Å | Mutation | Yes | [1] |
| PDB Sequence |
KQKNRPNRLI
27 VDEAINEDNS37 VVSLSQPKMD47 ELQLFRGDTV57 LLKGKKRREA67 VCIVLSDDAC 77 SDEKIRMNRV87 VRNNLRVRLG97 DVISIQPCPD107 VKYGKRIHVL117 PIDDTVEGIT 127 GNLFEVYLKP137 YFLEAYRPIR147 KGDIFLVRGG157 MRAVEFKVVE167 TDPSPYCIVA 177 PDTVIHCEGE187 PIKREDEEES197 LNEVGYDDIG207 GCRKQLAQIK217 EMVELPLRHP 227 ALFKAIGVKP237 PRGILLYGPP247 GTGKTLIARA257 VANETGAFFF267 LINGPEIMSK 277 LAGESESNLR287 KAFEEAEKNA297 PAIIFIDELD307 AIAPKREKTH317 GEVERRIVSQ 327 LLTLMDGLKQ337 RAHVIVMAAT347 NRPNSIDPAL357 RRFGRFDREV367 DIGIPDATGR 377 LEILQIHTKN387 MKLADDVDLE397 QVANETHGHV407 GADLAALCSE417 AALQAIRKKM 427 DLIDLEDETI437 DAEVMNSLAV447 TMDDFRWALS457 QSNPSALRET467 VVEVPQVTWE 477 DIGGLEDVKR487 ELQELVQYPV497 EHPDKFLKFG507 MTPSKGVLFY517 GPPGCGKTLL 527 AKAIANECQA537 NFISIKGPEL547 LTMWFGESEA557 NVREIFDKAR567 QAAPCVLFFD 577 ELDSIAKARG587 GNIGDGGGAA597 DRVINQILTE607 MDGMSTKKNV617 FIIGATNRPD 627 IIDPAILRPG637 RLDQLIYIPL647 PDEKSRVAIL657 KANLRKSPVA667 KDVDLEFLAK 677 MTNGFSGADL687 TEICQRACKL697 AIRESIESEI707 RRERERQTEE724 DDPVPEIRRD 734 HFEEAMRFAR744 RSVSDNDIRK754 YEMFAQTLQQ764 SR
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| PDB ID: 7BPB Human AAA+ ATPase VCP mutant - T76E, AMP-PNP bound form, Conformation I | ||||||
| Method | Electron microscopy | Resolution | 4.30 Å | Mutation | Yes | [1] |
| PDB Sequence |
KNRPNRLIVD
29 EAINEDNSVV39 SLSQPKMDEL49 QLFRGDTVLL59 KGKKRREAVC69 IVLSDDECSD 79 EKIRMNRVVR89 NNLRVRLGDV99 ISIQPCPDVK109 YGKRIHVLPI119 DDTVEGITGN 129 LFEVYLKPYF139 LEAYRPIRKG149 DIFLVRGGMR159 AVEFKVVETD169 PSPYCIVAPD 179 TVIHCEGEPI189 KREDEEESLN199 EVGYDDIGGC209 RKQLAQIKEM219 VELPLRHPAL 229 FKAIGVKPPR239 GILLYGPPGT249 GKTLIARAVA259 NETGAFFFLI269 NGPEIMSKLA 279 GESESNLRKA289 FEEAEKNAPA299 IIFIDELDAI309 APKREKTHGE319 VERRIVSQLL 329 TLMDGLKQRA339 HVIVMAATNR349 PNSIDPALRR359 FGRFDREVDI369 GIPDATGRLE 379 ILQIHTKNMK389 LADDVDLEQV399 ANETHGHVGA409 DLAALCSEAA419 LQAIRKKMDL 429 IDLEDETIDA439 EVMNSLAVTM449 DDFRWALSQS459 NPSALRETVV469 EVPQVTWEDI 479 GGLEDVKREL489 QELVQYPVEH499 PDKFLKFGMT509 PSKGVLFYGP519 PGCGKTLLAK 529 AIANECQANF539 ISIKGPELLT549 MWFGESEANV559 REIFDKARQA569 APCVLFFDEL 579 DSIAKARGGN589 IGDGGGAADR599 VINQILTEMD609 GMSTKKNVFI619 IGATNRPDII 629 DPAILRPGRL639 DQLIYIPLPD649 EKSRVAILKA659 NLRKSPVAKD669 VDLEFLAKMT 679 NGFSGADLTE689 ICQRACKLAI699 RESIESEIRR709 ERERQTEEDD726 PVPEIRRDHF 736 EEAMRFARRS746 VSDNDIRKYE756 MFAQTLQQSR766
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| PDB ID: 5KIY p97 ND1-A232E in complex with VIMP | ||||||
| Method | X-ray diffraction | Resolution | 2.79 Å | Mutation | Yes | [2] |
| PDB Sequence |
DDLSTAILKQ
19 KNRPNRLIVD29 EAINEDNSVV39 SLSQPKMDEL49 QLFRGDTVLL59 KGKKRREAVC 69 IVLSDDTCSD79 EKIRMNRVVR89 NNLRVRLGDV99 ISIQPCPDVK109 YGKRIHVLPI 119 DDTVEGITGN129 LFEVYLKPYF139 LEAYRPIRKG149 DIFLVRGGMR159 AVEFKVVETD 169 PSPYCIVAPD179 TVIHCEGEPI189 KREDEEESLN199 EVGYDDIGGC209 RKQLAQIKEM 219 VELPLRHPAL229 FKEIGVKPPR239 GILLYGPPGT249 GKTLIARAVA259 NETGAFFFLI 269 NGPEIMSKLA279 GESESNLRKA289 FEEAEKNAPA299 IIFIDELDAI309 APKREKTHGE 319 VERRIVSQLL329 TLMDGLKQRA339 HVIVMAATNR349 PNSIDPALRR359 FGRFDREVDI 369 GIPDATGRLE379 ILQIHTKNMK389 LADDVDLEQV399 ANETHGHVGA409 DLAALCSEAA 419 LQAIRKKMDL429 IDLEDETIDA439 EVMNSLAVTM449 DDFRWALSQS459 NRSH |
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ASP205
3.572
ILE206
3.811
GLY207
2.899
CYS209
4.085
GLY245
4.695
PRO246
4.323
PRO247
3.646
GLY248
3.200
THR249
3.235
GLY250
3.180
LYS251
2.787
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| PDB ID: 5KIW p97 ND1-L198W in complex with VIMP | ||||||
| Method | X-ray diffraction | Resolution | 3.41 Å | Mutation | Yes | [2] |
| PDB Sequence |
NRPNRLIVDE
30 AINEDNSVVS40 LSQPKMDELQ50 LFRGDTVLLK60 GKKRREAVCI70 VLSDDTCSDE 80 KIRMNRVVRN90 NLRVRLGDVI100 SIQPCPDVKY110 GKRIHVLPID120 DTVEGITGNL 130 FEVYLKPYFL140 EAYRPIRKGD150 IFLVRGGMRA160 VEFKVVETDP170 SPYCIVAPDT 180 VIHCEGEPIK190 REDEEESWNE200 VGYDDIGGCR210 KQLAQIKEMV220 ELPLRHPALF 230 KAIGVKPPRG240 ILLYGPPGTG250 KTLIARAVAN260 ETGAFFFLIN270 GPEIMSKLAG 280 ESESNLRKAF290 EEAEKNAPAI300 IFIDELDAIA310 PKREKTHGEV320 ERRIVSQLLT 330 LMDGLKQRAH340 VIVMAATNRP350 NSIDPALRRF360 GRFDREVDIG370 IPDATGRLEI 380 LQIHTKNMKL390 ADDVDLEQVA400 NETHGHVGAD410 LAALCSEAAL420 QAIRKKMDLI 430 DLEDETIDAE440 VMNSLAVTMD450 DFRWALSQSN460
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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 .ANP or .ANP2 or .ANP3 or :3ANP;style chemicals stick;color identity;select .A:205 or .A:206 or .A:207 or .A:209 or .A:246 or .A:247 or .A:248 or .A:249 or .A:250 or .A:251 or .A:252 or .A:253 or .A:304 or .A:305 or .A:348 or .A:380 or .A:383 or .A:384 or .A:408 or .A:409 or .A:412; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ASP205
3.517
ILE206
3.740
GLY207
2.926
CYS209
4.518
PRO246
3.975
PRO247
3.255
GLY248
3.200
THR249
2.940
GLY250
3.202
LYS251
2.642
THR252
2.255
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | The phosphorylation and dephosphorylation switch of VCP/p97 regulates the architecture of centrosome and spindle. Cell Death Differ. 2022 Oct;29(10):2070-2088. | ||||
| REF 2 | Structural basis for nucleotide-modulated p97 association with the ER membrane. Cell Discov. 2017 Dec 12;3:17045. | ||||
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