Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T55922 | Target Info | |||
| Target Name | S-adenosylmethionine decarboxylase proenzyme (AMD1) | ||||
| Synonyms | SamDC; S-adenosylmethioninedecarboxylase; AdoMetDC; AMD | ||||
| Target Type | Successful Target | ||||
| Gene Name | AMD1 | ||||
| Biochemical Class | Carbon-carbon lyase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | S-Adenosylmethionine methyl ester | Ligand Info | |||
| Canonical SMILES | COC(=O)C(CC[S+](C)CC1C(C(C(O1)N2C=NC3=C(N=CN=C32)N)O)O)N | ||||
| InChI | 1S/C16H25N6O5S/c1-26-16(25)8(17)3-4-28(2)5-9-11(23)12(24)15(27-9)22-7-21-10-13(18)19-6-20-14(10)22/h6-9,11-12,15,23-24H,3-5,17H2,1-2H3,(H2,18,19,20)/q+1/t8-,9+,11+,12+,15+,28?/m0/s1 | ||||
| InChIKey | HTMUWGYJLZAWHB-PIBDHAAFSA-N | ||||
| PubChem Compound ID | 446208 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 1I7B HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE WITH COVALENTLY BOUND PYRUVOYL GROUP AND COVALENTLY BOUND S-ADENOSYLMETHIONINE METHYL ESTER | ||||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [1] |
| PDB Sequence |
> Chain A
SMFVSKRRFI 78 LKTCGTTLLL88 KALVPLLKLA98 RDYSGFDSIQ108 SFFYSRKNFM118 KPSHQGYPHR 128 NFQEEIEFLN138 AIFPNGAGYC148 MGRMNSDCWY158 LYTLDFPESQ172 PDQTLEILMS 182 ELDPAVMDQF192 YMKDGVTAKD202 VTRESGIRDL212 IPGSVIDATM222 FNPCGYSMNG 232 MKSDGTYWTI242 HITPEPEFSY252 VSFETNLSQT262 SYDDLIRKVV272 EVFKPGKFVT 282 TLFVNQSSKC292 PQKIEGFKRL308 DCQSAMFNDY318 NFVFTSFAKK328 > Chain B AHFFEGTEKL 13 LEVWFSRQQP23 QGSGDLRTIP36 RSEWDILLKD46 VQCSIISVTK56 TDKQEAYVLS 66 E
|
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|
|
SER69[A]
3.571
LYS80[A]
4.754
THR81[A]
3.615
CYS82[A]
3.188
THR85[A]
3.688
PHE223[A]
3.427
ASN224[A]
3.161
PRO225[A]
4.905
CYS226[A]
3.054
GLY227[A]
3.440
TYR228[A]
3.368
SER229[A]
3.106
|
|||||
| PDB ID: 3DZ3 Human AdoMetDC F223A mutant with covalently bound S-Adenosylmethionine methyl ester | ||||||
| Method | X-ray diffraction | Resolution | 2.62 Å | Mutation | Yes | [2] |
| PDB Sequence |
> Chain A
SMFVSKRRFI 78 LKTCGTTLLL88 KALVPLLKLA98 RDYSGFDSIQ108 SFFYSRKNFM118 KPSHQGYPHR 128 NFQEEIEFLN138 AIFPNGAAYC148 MGRMNSDCWY158 LYTLDFPEQP173 DQTLEILMSE 183 LDPAVMDQFY193 MKDGVTAKDV203 TRESGIRDLI213 PGSVIDATMA223 NPCGYSMNGM 233 KSDGTYWTIH243 ITPEPEFSYV253 SFETNLSQTS263 YDDLIRKVVE273 VFKPGKFVTT 283 LFVNQQKIEG304 FKRLDCQSAM314 FNDYNFVFTS324 FAKK> Chain B AHFFEGTEKL 13 LEVWFSRQQP23 QGSGDLRTIP36 RSEWDILLKD46 VQCSIISVTK56 TDKQEAYVLS 66 E
|
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|
|
SER69[A]
3.606
LYS80[A]
4.798
THR81[A]
3.985
CYS82[A]
3.292
GLY83[A]
4.682
THR85[A]
3.958
ALA223[A]
4.034
ASN224[A]
4.232
CYS226[A]
3.090
GLY227[A]
3.453
TYR228[A]
2.995
|
|||||
| PDB ID: 3EP6 Human AdoMetDC D174N mutant complexed with S-Adenosylmethionine methyl ester and no putrescine bound | ||||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | Yes | [3] |
| PDB Sequence |
> Chain A
SMFVSKRRFI 78 LKTCGTTLLL88 KALVPLLKLA98 RDYSGFDSIQ108 SFFYSRKNFM118 KPSHQGYPHR 128 NFQEEIEFLN138 AIFPNGAAYC148 MGRMNSDCWY158 LYTLDFNQTL177 EILMSELDPA 187 VMDQFYMKDG197 VTAKDVTRES207 GIRDLIPGSV217 IDATMFNPCG227 YSMNGMKSDG 237 TYWTIHITPE247 PEFSYVSFET257 NLSQTSYDDL267 IRKVVEVFKP277 GKFVTTLFVN 287 QPQKIEGFKR307 LDCQSAMFND317 YNFVFTSFAK327 > Chain B AHFFEGTEKL 13 LEVWFSRGSG30 DLRTIPRSEW40 DILLKDVQCS50 IISVTKTDKQ60 EAYVLSE |
|||||
|
|
SER69[A]
3.607
LYS80[A]
4.880
THR81[A]
3.650
CYS82[A]
3.013
THR85[A]
3.897
PHE223[A]
3.531
ASN224[A]
3.178
PRO225[A]
4.908
CYS226[A]
3.217
GLY227[A]
3.403
TYR228[A]
3.257
SER229[A]
3.116
|
|||||
| PDB ID: 3EP8 Human AdoMetDC E178Q mutant complexed with S-Adenosylmethionine methyl ester and no putrescine bound | ||||||
| Method | X-ray diffraction | Resolution | 1.97 Å | Mutation | Yes | [3] |
| PDB Sequence |
> Chain A
SMFVSKRRFI 78 LKTCGTTLLL88 KALVPLLKLA98 RDYSGFDSIQ108 SFFYSRKNFM118 KPSHQGYPHR 128 NFQEEIEFLN138 AIFPNGAAYC148 MGRMNSDCWY158 LYTLDFPDQT176 LQILMSELDP 186 AVMDQFYMKD196 GVTAKDVTRE206 SGIRDLIPGS216 VIDATMFNPC226 GYSMNGMKSD 236 GTYWTIHITP246 EPEFSYVSFE256 TNLSQTSYDD266 LIRKVVEVFK276 PGKFVTTLFV 286 NQKIEGFKRL308 DCQSAMFNDY318 NFVFTSFAKK328 > Chain B AHFFEGTEKL 13 LEVWFSQGSG30 DLRTIPRSEW40 DILLKDVQCS50 IISVTKTDKQ60 EAYVLSE |
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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 .SMM or .SMM2 or .SMM3 or :3SMM;style chemicals stick;color identity;select .A:69 or .A:80 or .A:81 or .A:82 or .A:85 or .A:223 or .A:224 or .A:226 or .A:227 or .A:228 or .A:229 or .A:243 or .A:244 or .A:245 or .A:246 or .A:247 or .B:5 or .B:7 or .B:49 or .B:65 or .B:66 or .B:67; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
SER69[A]
3.608
LYS80[A]
4.796
THR81[A]
3.515
CYS82[A]
2.928
THR85[A]
4.048
PHE223[A]
3.631
ASN224[A]
3.453
CYS226[A]
3.295
GLY227[A]
3.508
TYR228[A]
3.263
SER229[A]
3.003
|
|||||
| PDB ID: 3EP7 Human AdoMetDC E256Q mutant complexed with S-Adenosylmethionine methyl ester and no putrescine bound | ||||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | Yes | [3] |
| PDB Sequence |
> Chain A
SMFVSKRRFI 78 LKTCGTTLLL88 KALVPLLKLA98 RDYSGFDSIQ108 SFFYSRKNFM118 KPSHQGYPHR 128 NFQEEIEFLN138 AIFPNGAAYC148 MGRMNSDCWY158 LYTLDFDQTL177 EILMSELDPA 187 VMDQFYMKDG197 VTAKDVTRES207 GIRDLIPGSV217 IDATMFNPCG227 YSMNGMKSDG 237 TYWTIHITPE247 PEFSYVSFQT257 NLSQTSYDDL267 IRKVVEVFKP277 GKFVTTLFVN 287 QKIEGFKRLD309 CQSAMFNDYN319 FVFTSFAKK> Chain B HFFEGTEKLL 14 EVWFSRQGSG30 DLRTIPRSEW40 DILLKDVQCS50 IISVTKTDKQ60 EAYVLSE |
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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 .SMM or .SMM2 or .SMM3 or :3SMM;style chemicals stick;color identity;select .A:69 or .A:80 or .A:81 or .A:82 or .A:85 or .A:223 or .A:224 or .A:226 or .A:227 or .A:228 or .A:229 or .A:243 or .A:244 or .A:245 or .A:246 or .A:247 or .B:5 or .B:7 or .B:49 or .B:65 or .B:66 or .B:67; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
SER69[A]
3.607
LYS80[A]
4.947
THR81[A]
3.508
CYS82[A]
2.944
THR85[A]
3.986
PHE223[A]
3.571
ASN224[A]
3.555
CYS226[A]
3.361
GLY227[A]
3.472
TYR228[A]
3.103
SER229[A]
3.092
|
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | The structural basis for substrate specificity and inhibition of human S-adenosylmethionine decarboxylase. Biochemistry. 2001 Aug 14;40(32):9484-94. | ||||
| REF 2 | New insights into the design of inhibitors of human S-adenosylmethionine decarboxylase: studies of adenine C8 substitution in structural analogues ... J Med Chem. 2009 Mar 12;52(5):1388-407. | ||||
| REF 3 | Structural basis for putrescine activation of human S-adenosylmethionine decarboxylase. Biochemistry. 2008 Dec 16;47(50):13404-17. | ||||
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