Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
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
DCAM_HUMAN
Drug Binding Sites of Target  Top
Ligand Name: Pyruvic acid Ligand Info
Structure Description Human AdoMetDC D174N mutant complexed with S-Adenosylmethionine methyl ester and no putrescine bound PDB:3EP6
Method X-ray diffraction Resolution 1.70 Å Mutation Yes [1]
PDB Sequence
> Chain A
SMFVSKRRFI
78
LKTCGTTLLL
88
KALVPLLKLA
98
RDYSGFDSIQ
108
SFFYSRKNFM
118

KPSHQGYPHR
128
NFQEEIEFLN
138
AIFPNGAAYC
148
MGRMNSDCWY
158
LYTLDFNQTL
177

EILMSELDPA
187
VMDQFYMKDG
197
VTAKDVTRES
207
GIRDLIPGSV
217
IDATMFNPCG
227

YSMNGMKSDG
237
TYWTIHITPE
247
PEFSYVSFET
257
NLSQTSYDDL
267
IRKVVEVFKP
277

GKFVTTLFVN
287
QPQKIEGFKR
307
LDCQSAMFND
317
YNFVFTSFAK
327

> Chain B
AHFFEGTEKL
13
LEVWFSRGSG
30
DLRTIPRSEW
40
DILLKDVQCS
50
IISVTKTDKQ
60

EAYVLSE
Residue
Distance (Å)
SER69[A]
1.362
MET70[A]
4.717
LYS80[A]
2.703
THR81[A]
3.501
CYS82[A]
4.174
Residue
Distance (Å)
SER229[A]
4.739
HIS243[A]
3.327
TYR63[B]
4.095
VAL64[B]
3.414
LEU65[B]
2.590
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: Urea Ligand Info
Structure Description Human AdoMetDC E178Q mutant with no putrescine bound PDB:3EP5
Method X-ray diffraction Resolution 1.99 Å Mutation Yes [1]
PDB Sequence
> Chain A
SMFVSKRRFI
78
LKTCGTTLLL
88
KALVPLLKLA
98
RDYSGFDSIQ
108
SFFYSRKNFM
118

KPSHQGYPHR
128
NFQEEIEFLN
138
AIFPNGAAYC
148
MGRMNSDCWY
158
LYTLDFPDQT
176

LQILMSELDP
186
AVMDQFYMKD
196
GVTAKDVTRE
206
SGIRDLIPGS
216
VIDATMFNPC
226

GYSMNGMKSD
236
GTYWTIHITP
246
EPEFSYVSFE
256
TNLSQTSYDD
266
LIRKVVEVFK
276

PGKFVTTLFV
286
NKIEGFKRLD
309
CQSAMFNDYN
319
FVFTSFAKK
> Chain B
HFFEGTEKLL
14
EVWFSRQGSG
30
DLRTIPRSEW
40
DILLKDVQCS
50
IISVTKTDKQ
60

EAYVLSE
Residue
Distance (Å)
PHE111[A]
3.875
SER113[A]
4.366
TRP157[A]
4.308
THR176[A]
3.710
GLN178[A]
4.559
Residue
Distance (Å)
PHE285[A]
4.063
PHE320[A]
4.936
LEU13[B]
3.794
GLU15[B]
3.561
Ligand Name: ORG 34517/34850 Ligand Info
Structure Description HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE WITH COVALENTLY BOUND PYRUVOYL GROUP AND COMPLEXED WITH 4-AMIDINOINDAN-1-ONE-2'-AMIDINOHYDRAZONE PDB:1I7M
Method X-ray diffraction Resolution 2.24 Å Mutation Yes [2]
PDB Sequence
> Chain A
SFVSKRRFIL
79
KTCGTTLLLK
89
ALVPLLKLAR
99
DYSGFDSIQS
109
FFYSRKNFKP
120

SHQGYPHRNF
130
QEEIEFLNAI
140
FPNGAGYCGR
151
NSDCWYLYTL
162
DFQPDQTLEI
179

LSELDPAVDQ
191
FYKDGVTAKD
202
VTRESGIRDL
212
IPGSVIDATF
223
NPCGYSNGKS
235

DGTYWTIHIT
245
PEPEFSYVSF
255
ETNLSQTSYD
265
DLIRKVVEVF
275
KPGKFVTTLF
285

VNQSSKCPQK
301
IEGFKRLDCQ
311
SAFNDYNFVF
322
TSFAKKQ
> Chain B
AHFFEGTEKL
13
LEVWFSRGSG
30
DLRTIPRSEW
40
DILLKDVQCS
50
IISVTKTDKQ
60

EAYVLSE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CG or .CG2 or .CG3 or :3CG;style chemicals stick;color identity;select .A:82 or .A:223 or .A:226 or .A:227 or .A:228 or .A:229 or .A:243 or .A:244 or .A:245 or .A:247 or .A:250 or .B:5 or .B:7 or .B:64 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
Residue
Distance (Å)
CYS82[A]
4.175
PHE223[A]
3.330
CYS226[A]
3.654
GLY227[A]
4.004
TYR228[A]
3.722
SER229[A]
2.839
HIS243[A]
3.629
ILE244[A]
2.982
THR245[A]
3.701
Residue
Distance (Å)
GLU247[A]
2.699
PHE250[A]
4.153
HIS5[B]
3.936
PHE7[B]
3.430
VAL64[B]
4.679
LEU65[B]
2.784
SER66[B]
2.727
GLU67[B]
3.238
Ligand Name: Putrescine Ligand Info
Structure Description Structure of a Human S-Adenosylmethionine Decarboxylase Self-processing Ester Intermediate and Mechanism of Putrescine Stimulation of Processing as Revealed by the H243A Mutant PDB:1JL0
Method X-ray diffraction Resolution 1.50 Å Mutation Yes [3]
PDB Sequence
HFFEGTEKLL
14
EVWFSRQQGS
29
GDLRTIPRSE
39
WDILLKDVQC
49
SIISVTKTDK
59

QEAYVLSESS
69
MFVSKRRFIL
79
KTCGTTLLLK
89
ALVPLLKLAR
99
DYSGFDSIQS
109

FFYSRKNFMK
119
PSHQGYPHRN
129
FQEEIEFLNA
139
IFPNGAGYCM
149
GRMNSDCWYL
159

YTLDFPVISQ
172
PDQTLEILMS
182
ELDPAVMDQF
192
YMKDGVTAKD
202
VTRESGIRDL
212

IPGSVIDATM
222
FNPCGYSMNG
232
MKSDGTYWTI
242
AITPEPEFSY
252
VSFETNLSQT
262

SYDDLIRKVV
272
EVFKPGKFVT
282
TLFVNQSSKC
292
QKIEGFKRLD
309
CQSAMFNDYN
319

FVFTSFAKKQ
329
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PUT or .PUT2 or .PUT3 or :3PUT;style chemicals stick;color identity;select .A:13 or .A:15 or .A:17 or .A:111 or .A:113 or .A:174 or .A:175 or .A:176 or .A:178 or .A:256 or .A:285 or .A:318; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LEU13
3.374
GLU15
2.788
TRP17
4.451
PHE111
3.645
SER113
4.321
ASP174
2.804
Residue
Distance (Å)
GLN175
4.701
THR176
2.755
GLU178
4.958
GLU256
4.945
PHE285
3.638
TYR318
3.601
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: [(2-aminooxyethyl)methylamino]-5'-deoxyadenosine Ligand Info
Structure Description HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE WITH COVALENTLY BOUND PYRUVOYL GROUP AND COVALENTLY BOUND 5'-DEOXY-5'-[N-METHYL-N-(2-AMINOOXYETHYL) AMINO]ADENOSINE PDB:1I72
Method X-ray diffraction Resolution 2.00 Å Mutation No [2]
PDB Sequence
> Chain A
SMFVSKRRFI
78
LKTCGTTLLL
88
KALVPLLKLA
98
RDYSGFDSIQ
108
SFFYSRKNFM
118

KPSHQGYPHR
128
NFQEEIEFLN
138
AIFPNGAGYC
148
MGRMNSDCWY
158
LYTLDFPESQ
172

PDQTLEILMS
182
ELDPAVMDQF
192
YMKDGVTAKD
202
VTRESGIRDL
212
IPGSVIDATM
222

FNPCGYSMNG
232
MKSDGTYWTI
242
HITPEPEFSY
252
VSFETNLSQT
262
SYDDLIRKVV
272

EVFKPGKFVT
282
TLFVNQSSKC
292
RPQKIEGFKR
307
LDCQSAMFND
317
YNFVFTSFAK
327

K
> Chain B
AHFFEGTEKL
13
LEVWFSRQQP
23
QGSGDLRTIP
36
RSEWDILLKD
46
VQCSIISVTK
56

TDKQEAYVLS
66
E
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MAO or .MAO2 or .MAO3 or :3MAO;style chemicals stick;color identity;select .A:69 or .A:80 or .A:82 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: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
Residue
Distance (Å)
SER69[A]
3.634
LYS80[A]
4.615
CYS82[A]
3.777
PHE223[A]
3.605
ASN224[A]
3.904
CYS226[A]
3.139
GLY227[A]
3.402
TYR228[A]
3.098
SER229[A]
3.097
HIS243[A]
3.478
Residue
Distance (Å)
ILE244[A]
3.334
THR245[A]
3.236
PRO246[A]
3.508
GLU247[A]
2.945
HIS5[B]
4.956
PHE7[B]
3.526
LEU65[B]
3.186
SER66[B]
3.151
GLU67[B]
2.711
Ligand Name: 5'-deoxy-5'-[(3-hydrazinopropyl)methylamino]adenosine Ligand Info
Structure Description HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE WITH COVALENTLY BOUND PYRUVOYL GROUP AND COVALENTLY BOUND 5'-DEOXY-5'-[(3-HYDRAZINOPROPYL)METHYLAMINO]ADENOSINE PDB:1I79
Method X-ray diffraction Resolution 2.01 Å Mutation No [2]
PDB Sequence
> Chain A
SMFVSKRRFI
78
LKTCGTTLLL
88
KALVPLLKLA
98
RDYSGFDSIQ
108
SFFYSRKNFM
118

KPSHQGYPHR
128
NFQEEIEFLN
138
AIFPNGAGYC
148
MGRMNSDCWY
158
LYTLDFPESQ
172

PDQTLEILMS
182
ELDPAVMDQF
192
YMKDGVTAKD
202
VTRESGIRDL
212
IPGSVIDATM
222

FNPCGYSMNG
232
MKSDGTYWTI
242
HITPEPEFSY
252
VSFETNLSQT
262
SYDDLIRKVV
272

EVFKPGKFVT
282
TLFVNQSSKC
292
RPQKIEGFKR
307
LDCQSAMFND
317
YNFVFTSFAK
327

K
> Chain B
AHFFEGTEKL
13
LEVWFSRQQP
23
QGSGDLRTIP
36
RSEWDILLKD
46
VQCSIISVTK
56

TDKQEAYVLS
66
E
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MHZ or .MHZ2 or .MHZ3 or :3MHZ;style chemicals stick;color identity;select .A:69 or .A:80 or .A:82 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:64 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
Residue
Distance (Å)
SER69[A]
3.624
LYS80[A]
4.738
CYS82[A]
3.269
PHE223[A]
3.484
ASN224[A]
4.128
CYS226[A]
3.198
GLY227[A]
3.397
TYR228[A]
3.061
SER229[A]
2.820
HIS243[A]
3.699
Residue
Distance (Å)
ILE244[A]
3.460
THR245[A]
3.428
PRO246[A]
3.350
GLU247[A]
2.840
HIS5[B]
4.891
PHE7[B]
3.452
VAL64[B]
4.552
LEU65[B]
2.635
SER66[B]
2.852
GLU67[B]
2.677
Ligand Name: MGBG Ligand Info
Structure Description HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE WITH COVALENTLY BOUND PYRUVOYL GROUP AND COMPLEXED WITH METHYLGLYOXAL BIS-(GUANYLHYDRAZONE) PDB:1I7C
Method X-ray diffraction Resolution 2.40 Å Mutation No [2]
PDB Sequence
> Chain A
SMFVSKRRFI
78
LKTCGTTLLL
88
KALVPLLKLA
98
RDYSGFDSIQ
108
SFFYSRKNFM
118

KPSHQGYPHR
128
NFQEEIEFLN
138
AIFPNGAGYC
148
MGRMNSDCWY
158
LYTLDFPESR
168

VISQPDQTLE
178
ILMSELDPAV
188
MDQFYMKDGV
198
TAKDVTRESG
208
IRDLIPGSVI
218

DATMFNPCGY
228
SMNGMKSDGT
238
YWTIHITPEP
248
EFSYVSFETN
258
LSQTSYDDLI
268

RKVVEVFKPG
278
KFVTTLFVNQ
288
STVLASPQKI
302
EGFKRLDCQS
312
AMFNDYNFVF
322

TSFAKKQ
> Chain B
AHFFEGTEKL
13
LEVWFSRQQP
23
QGSGDLRTIP
36
RSEWDILLKD
46
VQCSIISVTK
56

TDKQEAYVLS
66
E
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MGB or .MGB2 or .MGB3 or :3MGB;style chemicals stick;color identity;select .A:82 or .A:223 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 .A:250 or .B:7 or .B:64 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
Residue
Distance (Å)
CYS82[A]
4.024
PHE223[A]
3.179
CYS226[A]
3.303
GLY227[A]
3.750
TYR228[A]
3.656
SER229[A]
2.584
HIS243[A]
4.230
ILE244[A]
3.168
THR245[A]
3.418
Residue
Distance (Å)
PRO246[A]
4.525
GLU247[A]
2.809
PHE250[A]
4.743
PHE7[B]
3.723
VAL64[B]
4.552
LEU65[B]
2.734
SER66[B]
3.096
GLU67[B]
3.877
Ligand Name: 5'-Deoxy-5'-(N,N-dimethylamino)-8-methyladenosine Ligand Info
Structure Description Human AdoMetDC with 5'-Deoxy-5'-[(N-dimethyl)amino]-8-methyl-adenosine PDB:3H0W
Method X-ray diffraction Resolution 1.81 Å Mutation No [4]
PDB Sequence
> Chain A
SMFVSKRRFI
78
LKTCGTTLLL
88
KALVPLLKLA
98
RDYSGFDSIQ
108
SFFYSRKNFM
118

KPSHQGYPHR
128
NFQEEIEFLN
138
AIFPNGAAYC
148
MGRMNSDCWY
158
LYTLDFDQTL
177

EILMSELDPA
187
VMDQFYMKDG
197
VTAKDVTRES
207
GIRDLIPGSV
217
IDATMFNPCG
227

YSMNGMKSDG
237
TYWTIHITPE
247
PEFSYVSFET
257
NLSQTSYDDL
267
IRKVVEVFKP
277

GKFVTTLFVN
287
QKIEGFKRLD
309
CQSAMFNDYN
319
FVFTSFAK
> Chain B
AHFFEGTEKL
13
LEVWFSRQQP
23
QGSGDLRTIP
36
RSEWDILLKD
46
VQCSIISVTK
56

TDKQEAYVLS
66
E
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .N8M or .N8M2 or .N8M3 or :3N8M;style chemicals stick;color identity;select .A:82 or .A:223 or .A:224 or .A:225 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:66 or .B:67; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
CYS82[A]
3.495
PHE223[A]
3.511
ASN224[A]
3.482
PRO225[A]
4.074
CYS226[A]
3.198
GLY227[A]
3.410
TYR228[A]
3.249
SER229[A]
3.232
HIS243[A]
4.623
Residue
Distance (Å)
ILE244[A]
3.347
THR245[A]
3.368
PRO246[A]
3.464
GLU247[A]
2.628
HIS5[B]
4.441
PHE7[B]
3.647
SER66[B]
2.948
GLU67[B]
3.015
Ligand Name: 5'-{[4-(Aminooxy)butyl](methyl)amino}-5'-deoxy-8-ethenyladenosine Ligand Info
Structure Description Human AdoMetDC with 5'-[(4-aminooxybutyl)methylamino]-5'deoxy-8-ethyladenosine PDB:3DZ6
Method X-ray diffraction Resolution 1.83 Å Mutation No [5]
PDB Sequence
> Chain A
SMFVSKRRFI
78
LKTCGTTLLL
88
KALVPLLKLA
98
RDYSGFDSIQ
108
SFFYSRKNFM
118

KPSHQGYPHR
128
NFQEEIEFLN
138
AIFPNGAAYC
148
MGRMNSDCWY
158
LYTLDFDQTL
177

EILMSELDPA
187
VMDQFYMKDG
197
VTAKDVTRES
207
GIRDLIPGSV
217
IDATMFNPCG
227

YSMNGMKSDG
237
TYWTIHITPE
247
PEFSYVSFET
257
NLSQTSYDDL
267
IRKVVEVFKP
277

GKFVTTLFVN
287
IEGFKRLDCQ
311
SAMFNDYNFV
321
FTSFAKK
> Chain B
HFFEGTEKLL
14
EVWFSRGSGD
31
LRTIPRSEWD
41
ILLKDVQCSI
51
ISVTKTDKQE
61

AYVLSE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .M8E or .M8E2 or .M8E3 or :3M8E;style chemicals stick;color identity;select .A:82 or .A:85 or .A:223 or .A:224 or .A:225 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
Residue
Distance (Å)
CYS82[A]
3.117
THR85[A]
4.847
PHE223[A]
3.608
ASN224[A]
3.372
PRO225[A]
3.650
CYS226[A]
3.251
GLY227[A]
3.488
TYR228[A]
3.134
SER229[A]
3.323
HIS243[A]
4.475
Residue
Distance (Å)
ILE244[A]
3.162
THR245[A]
3.376
PRO246[A]
3.415
GLU247[A]
2.666
HIS5[B]
4.236
PHE7[B]
3.551
CYS49[B]
3.778
LEU65[B]
2.956
SER66[B]
2.961
GLU67[B]
2.979
Ligand Name: 3-[{[(2r,3s,4r,5r)-5-(6-Amino-8-Methyl-9h-Purin-9-Yl)-3,4-Dihydroxytetrahydrofuran-2-Yl]methyl}(Methyl)amino]propanamide Ligand Info
Structure Description Human AdoMetDC with 5'-[(2-carboxamidoethyl)methylamino]-5'-deoxy-8-methyladenosine PDB:3DZ4
Method X-ray diffraction Resolution 1.84 Å Mutation No [5]
PDB Sequence
> Chain A
SMFVSKRRFI
78
LKTCGTTLLL
88
KALVPLLKLA
98
RDYSGFDSIQ
108
SFFYSRKNFM
118

KPSHQGYPHR
128
NFQEEIEFLN
138
AIFPNGAAYC
148
MGRMNSDCWY
158
LYTLDFSQPD
174

QTLEILMSEL
184
DPAVMDQFYM
194
KDGVTAKDVT
204
RESGIRDLIP
214
GSVIDATMFN
224

PCGYSMNGMK
234
SDGTYWTIHI
244
TPEPEFSYVS
254
FETNLSQTSY
264
DDLIRKVVEV
274

FKPGKFVTTL
284
FVNQSSKCRK
301
IEGFKRLDCQ
311
SAMFNDYNFV
321
FTSFAK
> Chain B
AHFFEGTEKL
13
LEVWFSRQQP
23
QGSGDLRTIP
36
RSEWDILLKD
46
VQCSIISVTK
56

TDKQEAYVLS
66
E
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .C8M or .C8M2 or .C8M3 or :3C8M;style chemicals stick;color identity;select .A:82 or .A:223 or .A:224 or .A:225 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: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
Residue
Distance (Å)
CYS82[A]
3.376
PHE223[A]
3.224
ASN224[A]
3.215
PRO225[A]
4.236
CYS226[A]
3.236
GLY227[A]
3.271
TYR228[A]
3.372
SER229[A]
2.921
HIS243[A]
3.824
Residue
Distance (Å)
ILE244[A]
3.318
THR245[A]
3.513
PRO246[A]
3.428
GLU247[A]
2.833
HIS5[B]
4.435
PHE7[B]
3.664
LEU65[B]
3.008
SER66[B]
3.007
GLU67[B]
3.082
Ligand Name: 5'-[(3-Aminopropyl)(Methyl)amino]-5'-Deoxy-8-Methyladenosine Ligand Info
Structure Description Human AdoMetDC with 5'-[(3-aminopropyl)methylamino]-5'deoxy-8-methyladenosine PDB:3DZ2
Method X-ray diffraction Resolution 1.86 Å Mutation No [5]
PDB Sequence
> Chain A
SMFVSKRRFI
78
LKTCGTTLLL
88
KALVPLLKLA
98
RDYSGFDSIQ
108
SFFYSRKNFM
118

KPSHQGYPHR
128
NFQEEIEFLN
138
AIFPNGAAYC
148
MGRMNSDCWY
158
LYTLDFPESQ
172

PDQTLEILMS
182
ELDPAVMDQF
192
YMKDGVTAKD
202
VTRESGIRDL
212
IPGSVIDATM
222

FNPCGYSMNG
232
MKSDGTYWTI
242
HITPEPEFSY
252
VSFETNLSQT
262
SYDDLIRKVV
272

EVFKPGKFVT
282
TLFVNQSSKC
292
EGFKRLDCQS
312
AMFNDYNFVF
322
TSFAK
> Chain B
AHFFEGTEKL
13
LEVWFSRQQQ
27
GSGDLRTIPR
37
SEWDILLKDV
47
QCSIISVTKT
57

DKQEAYVLSE
67
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .A8M or .A8M2 or .A8M3 or :3A8M;style chemicals stick;color identity;select .A:82 or .A:223 or .A:224 or .A:225 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:9 or .B:11 or .B:66 or .B:67; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
CYS82[A]
2.964
PHE223[A]
3.637
ASN224[A]
3.248
PRO225[A]
3.895
CYS226[A]
3.166
GLY227[A]
3.124
TYR228[A]
3.191
SER229[A]
3.467
HIS243[A]
3.229
ILE244[A]
3.092
Residue
Distance (Å)
THR245[A]
3.402
PRO246[A]
3.407
GLU247[A]
2.869
HIS5[B]
4.546
PHE7[B]
3.579
GLY9[B]
4.294
GLU11[B]
3.310
SER66[B]
2.779
GLU67[B]
3.093
Ligand Name: 2-[{[(2r,3s,4r,5r)-5-(6-Amino-8-Methyl-9h-Purin-9-Yl)-3,4-Dihydroxytetrahydrofuran-2-Yl]methyl}(Methyl)amino]acetamide Ligand Info
Structure Description Human AdoMetDC with 5'-[(carboxamidomethyl)methylamino]-5'-deoxy-8-methyladenosine PDB:3DZ7
Method X-ray diffraction Resolution 1.91 Å Mutation No [5]
PDB Sequence
> Chain A
SMFVSKRRFI
78
LKTCGTTLLL
88
KALVPLLKLA
98
RDYSGFDSIQ
108
SFFYSRKNFM
118

KPSHQGYPHR
128
NFQEEIEFLN
138
AIFPNGAAYC
148
MGRMNSDCWY
158
LYTLDFPDQT
176

LEILMSELDP
186
AVMDQFYMKD
196
GVTAKDVTRE
206
SGIRDLIPGS
216
VIDATMFNPC
226

GYSMNGMKSD
236
GTYWTIHITP
246
EPEFSYVSFE
256
TNLSQTSYDD
266
LIRKVVEVFK
276

PGKFVTTLFV
286
NQSSKCIEGF
305
KRLDCQSAMF
315
NDYNFVFTSF
325
AK
> Chain B
AHFFEGTEKL
13
LEVWFSRQQP
23
QGSGDLRTIP
36
RSEWDILLKD
46
VQCSIISVTK
56

TDKQEAYVLS
66
E
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .O8M or .O8M2 or .O8M3 or :3O8M;style chemicals stick;color identity;select .A:82 or .A:223 or .A:224 or .A:225 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:9 or .B:11 or .B:66 or .B:67; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
CYS82[A]
3.110
PHE223[A]
3.680
ASN224[A]
3.012
PRO225[A]
3.945
CYS226[A]
3.048
GLY227[A]
3.551
TYR228[A]
3.268
SER229[A]
3.299
HIS243[A]
3.067
ILE244[A]
3.328
Residue
Distance (Å)
THR245[A]
3.245
PRO246[A]
3.606
GLU247[A]
2.851
HIS5[B]
4.487
PHE7[B]
3.617
GLY9[B]
4.186
GLU11[B]
4.872
SER66[B]
2.744
GLU67[B]
3.298
Ligand Name: Selenomethionine Ligand Info
Structure Description HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE WITH COVALENTLY BOUND PYRUVOYL GROUP AND COMPLEXED WITH 4-AMIDINOINDAN-1-ONE-2'-AMIDINOHYDRAZONE PDB:1I7M
Method X-ray diffraction Resolution 2.24 Å Mutation Yes [2]
PDB Sequence
> Chain A
SFVSKRRFIL
79
KTCGTTLLLK
89
ALVPLLKLAR
99
DYSGFDSIQS
109
FFYSRKNFKP
120

SHQGYPHRNF
130
QEEIEFLNAI
140
FPNGAGYCGR
151
NSDCWYLYTL
162
DFQPDQTLEI
179

LSELDPAVDQ
191
FYKDGVTAKD
202
VTRESGIRDL
212
IPGSVIDATF
223
NPCGYSNGKS
235

DGTYWTIHIT
245
PEPEFSYVSF
255
ETNLSQTSYD
265
DLIRKVVEVF
275
KPGKFVTTLF
285

VNQSSKCPQK
301
IEGFKRLDCQ
311
SAFNDYNFVF
322
TSFAKKQ
> Chain B
AHFFEGTEKL
13
LEVWFSRGSG
30
DLRTIPRSEW
40
DILLKDVQCS
50
IISVTKTDKQ
60

EAYVLSE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MSE or .MSE2 or .MSE3 or :3MSE;style chemicals stick;color identity;select .A:69 or .A:71 or .A:72 or .A:77 or .A:78 or .A:79 or .A:116 or .A:117 or .A:119 or .A:120 or .A:147 or .A:148 or .A:150 or .A:151 or .A:153 or .A:154 or .A:155 or .A:156 or .A:157 or .A:158 or .A:179 or .A:180 or .A:182 or .A:183 or .A:184 or .A:185 or .A:186 or .A:187 or .A:188 or .A:190 or .A:191 or .A:192 or .A:193 or .A:195 or .A:196 or .A:199 or .A:200 or .A:203 or .A:209 or .A:215 or .A:216 or .A:217 or .A:218 or .A:219 or .A:220 or .A:221 or .A:223 or .A:224 or .A:225 or .A:226 or .A:227 or .A:228 or .A:229 or .A:231 or .A:232 or .A:234 or .A:235 or .A:238 or .A:239 or .A:240 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:246 or .A:250 or .A:251 or .A:252 or .A:253 or .A:254 or .A:255 or .A:271 or .A:272 or .A:275 or .A:277 or .A:279 or .A:280 or .A:311 or .A:312 or .A:313 or .A:315 or .A:316 or .A:317 or .A:318 or .A:319 or .A:320 or .A:322 or .B:6 or .B:7 or .B:8 or .B:9 or .B:10 or .B:40 or .B:44 or .B:51 or .B:55 or .B:56 or .B:57 or .B:60 or .B:61 or .B:62 or .B:63 or .B:64 or .B:65; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
SER69[A]
1.335
PHE71[A]
1.327
VAL72[A]
4.063
PHE77[A]
3.570
ILE78[A]
3.302
LEU79[A]
4.089
ASN116[A]
3.927
PHE117[A]
1.325
LYS119[A]
1.333
PRO120[A]
3.532
TYR147[A]
3.496
CYS148[A]
1.329
GLY150[A]
1.326
ARG151[A]
1.325
ASN153[A]
1.327
SER154[A]
3.214
ASP155[A]
4.724
CYS156[A]
3.578
TRP157[A]
2.705
TYR158[A]
4.902
ILE179[A]
3.463
LEU180[A]
1.326
SER182[A]
1.328
GLU183[A]
4.748
LEU184[A]
3.766
ASP185[A]
3.040
PRO186[A]
2.929
ALA187[A]
3.345
VAL188[A]
1.332
ASP190[A]
1.336
GLN191[A]
3.106
PHE192[A]
2.938
TYR193[A]
1.335
LYS195[A]
1.330
ASP196[A]
4.345
THR199[A]
4.580
ALA200[A]
3.594
VAL203[A]
3.705
ILE209[A]
4.401
GLY215[A]
4.206
SER216[A]
3.085
VAL217[A]
2.721
ILE218[A]
3.803
ASP219[A]
3.124
ALA220[A]
3.872
THR221[A]
1.322
PHE223[A]
1.331
ASN224[A]
3.515
PRO225[A]
2.866
CYS226[A]
4.455
GLY227[A]
3.254
TYR228[A]
3.413
SER229[A]
1.324
Residue
Distance (Å)
ASN231[A]
1.334
GLY232[A]
1.323
LYS234[A]
1.327
SER235[A]
4.474
THR238[A]
3.208
TYR239[A]
4.332
TRP240[A]
3.352
THR241[A]
2.920
ILE242[A]
2.985
HIS243[A]
4.404
ILE244[A]
3.972
THR245[A]
4.603
PRO246[A]
3.484
PHE250[A]
3.564
SER251[A]
4.162
TYR252[A]
3.193
VAL253[A]
2.792
SER254[A]
4.417
PHE255[A]
4.010
VAL271[A]
3.582
VAL272[A]
4.883
PHE275[A]
3.666
PRO277[A]
3.564
LYS279[A]
3.620
PHE280[A]
3.649
GLN311[A]
3.723
SER312[A]
4.727
ALA313[A]
1.327
PHE315[A]
1.324
ASN316[A]
4.656
ASP317[A]
4.819
TYR318[A]
3.805
ASN319[A]
2.818
PHE320[A]
3.547
PHE322[A]
3.587
PHE6[B]
4.031
PHE7[B]
4.158
GLU8[B]
2.838
GLY9[B]
4.438
THR10[B]
4.894
TRP40[B]
3.466
LEU44[B]
4.120
ILE51[B]
4.536
THR55[B]
3.534
LYS56[B]
4.272
THR57[B]
3.205
GLN60[B]
3.478
GLU61[B]
3.548
ALA62[B]
3.515
TYR63[B]
2.739
VAL64[B]
4.995
LEU65[B]
4.311
Ligand Name: 5'-{[2-(Aminooxy)ethyl](Methyl)amino}-5'-Deoxy-8-Methyladenosine Ligand Info
Structure Description Human AdoMetDC with covalently bound 5'-[(2-aminooxyethyl)methylamino]-5'-deoxy-8-methyladenosine PDB:3DZ5
Method X-ray diffraction Resolution 2.43 Å Mutation No [5]
PDB Sequence
> Chain A
SMFVSKRRFI
78
LKTCGTTLLL
88
KALVPLLKLA
98
RDYSGFDSIQ
108
SFFYSRKNFM
118

KPSHQGYPHR
128
NFQEEIEFLN
138
AIFPNGAAYC
148
MGRMNSDCWY
158
LYTLDSQPDQ
175

TLEILMSELD
185
PAVMDQFYMK
195
DGVTAKDVTR
205
ESGIRDLIPG
215
SVIDATMFNP
225

CGYSMNGMKS
235
DGTYWTIHIT
245
PEPEFSYVSF
255
ETNLSQTSYD
265
DLIRKVVEVF
275

KPGKFVTTLF
285
VNQSSQKIEG
304
FKRLDCQSAM
314
FNDYNFVFTS
324
FAKK
> Chain B
AHFFEGTEKL
13
LEVWFGSGDL
32
RTIPRSEWDI
42
LLKDVQCSII
52
SVTKTDKQEA
62

YVLSE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .M8M or .M8M2 or .M8M3 or :3M8M;style chemicals stick;color identity;select .A:69 or .A:82 or .A:223 or .A:224 or .A:225 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:7 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
Residue
Distance (Å)
SER69[A]
3.663
CYS82[A]
3.923
PHE223[A]
3.546
ASN224[A]
3.163
PRO225[A]
4.428
CYS226[A]
3.270
GLY227[A]
3.162
TYR228[A]
3.149
SER229[A]
2.946
Residue
Distance (Å)
HIS243[A]
3.245
ILE244[A]
3.061
THR245[A]
3.368
PRO246[A]
3.242
GLU247[A]
2.750
PHE7[B]
3.482
LEU65[B]
3.030
SER66[B]
3.636
GLU67[B]
3.167
Ligand Name: 5'-Deoxy-5'-(dimethyl-lambda~4~-sulfanyl)adenosine Ligand Info
Structure Description Human AdoMetDC with 5'-Deoxy-5'-(dimethylsulfonio) adenosine PDB:3H0V
Method X-ray diffraction Resolution 2.24 Å Mutation No [4]
PDB Sequence
> Chain A
SMFVSKRRFI
78
LKTCGTTLLL
88
KALVPLLKLA
98
RDYSGFDSIQ
108
SFFYSRKNFM
118

KPSHQGYPHR
128
NFQEEIEFLN
138
AIFPNGAAYC
148
MGRMNSDCWY
158
LYTLDFPDQT
176

LEILMSELDP
186
AVMDQFYMKD
196
GVTAKDVTRE
206
SGIRDLIPGS
216
VIDATMFNPC
226

GYSMNGMKSD
236
GTYWTIHITP
246
EPEFSYVSFE
256
TNLSQTSYDD
266
LIRKVVEVFK
276

PGKFVTTLFV
286
NQKIEGFKRL
308
DCQSAMFNDY
318
NFVFTSFAK
> Chain B
HFFEGTEKLL
14
EVWFSRQQGS
29
GDLRTIPRSE
39
WDILLKDVQC
49
SIISVTKTDK
59

QEAYVLSE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .M2T or .M2T2 or .M2T3 or :3M2T;style chemicals stick;color identity;select .A:82 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:7 or .B:66 or .B:67; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
CYS82[A]
3.589
PHE223[A]
3.586
ASN224[A]
4.362
CYS226[A]
3.257
GLY227[A]
3.336
TYR228[A]
3.100
SER229[A]
3.112
HIS243[A]
4.175
Residue
Distance (Å)
ILE244[A]
3.122
THR245[A]
3.270
PRO246[A]
3.382
GLU247[A]
2.662
PHE7[B]
3.567
SER66[B]
3.322
GLU67[B]
3.174
Ligand Name: S-Adenosylmethionine methyl ester Ligand Info
Structure Description Human AdoMetDC D174N mutant complexed with S-Adenosylmethionine methyl ester and no putrescine bound PDB:3EP6
Method X-ray diffraction Resolution 1.70 Å Mutation Yes [1]
PDB Sequence
> Chain A
SMFVSKRRFI
78
LKTCGTTLLL
88
KALVPLLKLA
98
RDYSGFDSIQ
108
SFFYSRKNFM
118

KPSHQGYPHR
128
NFQEEIEFLN
138
AIFPNGAAYC
148
MGRMNSDCWY
158
LYTLDFNQTL
177

EILMSELDPA
187
VMDQFYMKDG
197
VTAKDVTRES
207
GIRDLIPGSV
217
IDATMFNPCG
227

YSMNGMKSDG
237
TYWTIHITPE
247
PEFSYVSFET
257
NLSQTSYDDL
267
IRKVVEVFKP
277

GKFVTTLFVN
287
QPQKIEGFKR
307
LDCQSAMFND
317
YNFVFTSFAK
327

> Chain B
AHFFEGTEKL
13
LEVWFSRGSG
30
DLRTIPRSEW
40
DILLKDVQCS
50
IISVTKTDKQ
60

EAYVLSE
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:225 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
Residue
Distance (Å)
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
Residue
Distance (Å)
HIS243[A]
3.864
ILE244[A]
3.466
THR245[A]
3.340
PRO246[A]
3.524
GLU247[A]
2.732
HIS5[B]
4.238
PHE7[B]
3.407
CYS49[B]
4.778
LEU65[B]
3.055
SER66[B]
3.319
GLU67[B]
2.958
Click to View More Binding Site Information of This Target and Ligand Pair
References  Top
REF 1 Structural basis for putrescine activation of human S-adenosylmethionine decarboxylase. Biochemistry. 2008 Dec 16;47(50):13404-17.
REF 2 The structural basis for substrate specificity and inhibition of human S-adenosylmethionine decarboxylase. Biochemistry. 2001 Aug 14;40(32):9484-94.
REF 3 Structure of a human S-adenosylmethionine decarboxylase self-processing ester intermediate and mechanism of putrescine stimulation of processing as revealed by the H243A mutant. Biochemistry. 2001 Aug 14;40(32):9495-504.
REF 4 Role of the sulfonium center in determining the ligand specificity of human s-adenosylmethionine decarboxylase. Biochemistry. 2009 Jul 14;48(27):6423-30.
REF 5 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.

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