Receptor
PDB id Resolution Class Description Source Keywords
3T7V 1.5 Å EC: 2.8.1.6 CRYSTAL STRUCTURE OF METHYLORNITHINE SYNTHASE (PYLB) METHANOSARCINA BARKERI TIM-BARREL FOLD MUTASE [4FE-4S]-CLUSTER SAM LYSINE 3- METHYLORNITHINE TRANSFERASE
Ref.: CRYSTAL STRUCTURE OF METHYLORNITHINE SYNTHASE (PYLB INSIGHTS INTO THE PYRROLYSINE BIOSYNTHESIS. ANGEW.CHEM.INT.ED.ENGL. V. 51 1339 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MD0 A:993;
Valid;
none;
submit data
146.188 C6 H14 N2 O2 C[C@H...
SAM A:992;
Valid;
none;
submit data
398.437 C15 H22 N6 O5 S C[S@@...
SF4 A:991;
Part of Protein;
none;
submit data
351.64 Fe4 S4 [S]12...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3T7V 1.5 Å EC: 2.8.1.6 CRYSTAL STRUCTURE OF METHYLORNITHINE SYNTHASE (PYLB) METHANOSARCINA BARKERI TIM-BARREL FOLD MUTASE [4FE-4S]-CLUSTER SAM LYSINE 3- METHYLORNITHINE TRANSFERASE
Ref.: CRYSTAL STRUCTURE OF METHYLORNITHINE SYNTHASE (PYLB INSIGHTS INTO THE PYRROLYSINE BIOSYNTHESIS. ANGEW.CHEM.INT.ED.ENGL. V. 51 1339 2012
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3T7V - SAM C15 H22 N6 O5 S C[S@@+](CC....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3T7V - SAM C15 H22 N6 O5 S C[S@@+](CC....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3T7V - SAM C15 H22 N6 O5 S C[S@@+](CC....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: MD0; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 MD0 1 1
2 SKJ 0.612903 0.724138
3 ILE 0.551724 0.655172
4 DAB 0.466667 0.827586
5 CUW 0.405405 0.727273
6 P4B 0.405405 0.714286
Ligand no: 2; Ligand: SAM; Similar ligands found: 246
No: Ligand ECFP6 Tc MDL keys Tc
1 SAM 1 1
2 SMM 0.792683 0.96
3 S4M 0.6875 0.909091
4 S7M 0.670455 0.945946
5 M2T 0.636364 0.878378
6 GEK 0.612903 0.931507
7 SAI 0.571429 0.878378
8 ADN 0.565789 0.773333
9 RAB 0.565789 0.773333
10 XYA 0.565789 0.773333
11 5CD 0.564103 0.783784
12 EP4 0.5625 0.826667
13 SA8 0.56044 0.945205
14 SFG 0.555556 0.875
15 5X8 0.555556 0.888889
16 5N5 0.551282 0.773333
17 A4D 0.544304 0.797297
18 EEM 0.542553 0.945946
19 SAH 0.537634 0.916667
20 EU9 0.537037 0.809524
21 DTA 0.536585 0.789474
22 62X 0.535354 0.884615
23 MTA 0.53012 0.875
24 3DH 0.517647 0.849315
25 AMP MG 0.517241 0.7375
26 5AL 0.510417 0.743902
27 VMS 0.510204 0.673913
28 54H 0.510204 0.673913
29 0UM 0.51 0.857143
30 NWW 0.506173 0.739726
31 LMS 0.505747 0.666667
32 AMP 0.505747 0.707317
33 A 0.505747 0.707317
34 45A 0.505618 0.753086
35 ABM 0.505618 0.753086
36 A5A 0.505155 0.688889
37 SSA 0.5 0.684783
38 5AD 0.5 0.75
39 SON 0.5 0.746988
40 6RE 0.5 0.78481
41 SRP 0.5 0.746988
42 K15 0.5 0.883117
43 LSS 0.49505 0.706522
44 CA0 0.494624 0.714286
45 AP2 0.494505 0.705882
46 A12 0.494505 0.705882
47 ME8 0.490385 0.841463
48 TSB 0.49 0.681319
49 5CA 0.49 0.684783
50 DAL AMP 0.49 0.765432
51 53H 0.49 0.666667
52 ACP 0.489362 0.694118
53 KG4 0.489362 0.714286
54 ADP 0.48913 0.690476
55 5AS 0.48913 0.648936
56 J7C 0.488889 0.772152
57 A2D 0.488889 0.690476
58 ZAS 0.488636 0.769231
59 8QN 0.485149 0.743902
60 9ZD 0.485149 0.729412
61 9ZA 0.485149 0.729412
62 8LH 0.484848 0.746988
63 GAP 0.484536 0.73494
64 AN2 0.483871 0.682353
65 A3S 0.483871 0.813333
66 ADP BEF 0.483871 0.728395
67 ADP MG 0.483871 0.728395
68 A7D 0.483871 0.851351
69 GJV 0.483516 0.775
70 SRA 0.483146 0.694118
71 GSU 0.480769 0.722222
72 KAA 0.480769 0.698925
73 LAD 0.480769 0.752941
74 DSZ 0.480392 0.703297
75 AMO 0.480392 0.746988
76 52H 0.48 0.666667
77 8LE 0.479592 0.717647
78 APC MG 0.479167 0.731707
79 M33 0.478723 0.722892
80 BA3 0.478261 0.690476
81 MAO 0.478261 0.82716
82 AOC 0.477778 0.776316
83 NEC 0.477778 0.75
84 DSH 0.477778 0.842105
85 SXZ 0.47619 0.894737
86 NVA LMS 0.475728 0.736264
87 AHX 0.475728 0.701149
88 Y3J 0.47561 0.706667
89 8LQ 0.475248 0.768293
90 QA7 0.475248 0.738095
91 G5A 0.474227 0.684783
92 A3T 0.473684 0.8
93 B4P 0.473118 0.690476
94 AP5 0.473118 0.690476
95 A3N 0.472527 0.766234
96 KB1 0.471698 0.833333
97 LEU LMS 0.471154 0.752809
98 PRX 0.46875 0.73494
99 APC 0.46875 0.705882
100 AT4 0.468085 0.686047
101 4AD 0.466019 0.759036
102 PAJ 0.466019 0.712644
103 NWQ 0.465909 0.767123
104 V2G 0.464646 0.701149
105 ATP MG 0.463918 0.728395
106 ADP PO3 0.463918 0.728395
107 ADV 0.463918 0.72619
108 RBY 0.463918 0.72619
109 ADX 0.463158 0.666667
110 MHZ 0.463158 0.82716
111 AU1 0.463158 0.674419
112 NB8 0.462264 0.72093
113 TXA 0.462264 0.72619
114 A3G 0.461538 0.802632
115 ANP MG 0.46 0.702381
116 VO4 ADP 0.46 0.694118
117 BEF ADP 0.459184 0.710843
118 VRT 0.459184 0.842105
119 XAH 0.458716 0.715909
120 KYE 0.458716 0.802469
121 YSA 0.458716 0.684783
122 50T 0.458333 0.682353
123 ATP 0.458333 0.690476
124 H1Q 0.458333 0.719512
125 HEJ 0.458333 0.690476
126 7D7 0.45679 0.723684
127 V47 0.455446 0.810811
128 KH3 0.455357 0.871795
129 ACQ 0.454545 0.694118
130 AR6 0.453608 0.710843
131 APR 0.453608 0.710843
132 5FA 0.453608 0.690476
133 AQP 0.453608 0.690476
134 NSS 0.451923 0.703297
135 FA5 0.449541 0.746988
136 AGS 0.44898 0.678161
137 A5D 0.44898 0.789474
138 AD9 0.44898 0.674419
139 PTJ 0.448598 0.72093
140 YLB 0.448276 0.758621
141 YLP 0.447368 0.738636
142 OZP 0.447368 0.844156
143 8X1 0.446602 0.680851
144 D3Y 0.446602 0.792208
145 N5O 0.445652 0.789474
146 ALF ADP 0.445545 0.678161
147 3AM 0.444444 0.674699
148 MYR AMP 0.444444 0.776471
149 HY8 0.443478 0.822785
150 OAD 0.443396 0.73494
151 2VA 0.443299 0.779221
152 KXW 0.442478 0.844156
153 QXP 0.442308 0.67033
154 S8M 0.442308 0.831169
155 OOB 0.442308 0.722892
156 6YZ 0.441176 0.694118
157 T99 0.44 0.686047
158 ANP 0.44 0.674419
159 TAT 0.44 0.686047
160 N37 0.439655 0.828947
161 WAQ 0.439252 0.75
162 HZ2 0.438596 0.822785
163 8PZ 0.436364 0.684783
164 B5Y 0.436364 0.717647
165 N5A 0.43617 0.786667
166 F0P 0.435897 0.844156
167 YLC 0.435897 0.755814
168 AAT 0.435644 0.797468
169 1ZZ 0.435185 0.755814
170 3OD 0.435185 0.73494
171 9K8 0.435185 0.663158
172 NVA 2AD 0.434343 0.855263
173 00A 0.433962 0.689655
174 DLL 0.433962 0.722892
175 7MD 0.433628 0.715909
176 ARG AMP 0.433628 0.727273
177 ATF 0.431373 0.666667
178 SO8 0.43 0.792208
179 A6D 0.429907 0.72619
180 QXG 0.429907 0.663043
181 9X8 0.429907 0.717647
182 3UK 0.429907 0.714286
183 F2R 0.429752 0.7
184 OZV 0.428571 0.690476
185 AMP DBH 0.428571 0.714286
186 5SV 0.428571 0.741176
187 TYM 0.42735 0.746988
188 WSA 0.42735 0.692308
189 9SN 0.427273 0.681818
190 AHZ 0.426087 0.755814
191 PR8 0.425926 0.744186
192 B5V 0.425926 0.705882
193 J4G 0.425926 0.759036
194 3NZ 0.425926 0.807692
195 P5A 0.425926 0.691489
196 R2V 0.425926 0.67033
197 A1R 0.424528 0.709302
198 2A5 0.424242 0.674419
199 Q34 0.423729 0.802469
200 7MC 0.423729 0.719101
201 Q2M 0.423729 0.846154
202 B5M 0.423423 0.717647
203 HQG 0.423077 0.702381
204 U4Y 0.422414 0.88
205 7D5 0.422222 0.658824
206 JB6 0.422018 0.709302
207 FYA 0.422018 0.722892
208 AYB 0.421488 0.75
209 JNT 0.420561 0.694118
210 K2H 0.420561 0.805195
211 B1U 0.419643 0.632653
212 MAP 0.419048 0.659091
213 KY2 0.419048 0.777778
214 A22 0.419048 0.682353
215 2AM 0.417582 0.666667
216 TAD 0.417391 0.712644
217 ADP BMA 0.416667 0.714286
218 A3P 0.416667 0.686747
219 25A 0.415094 0.690476
220 Q2V 0.413223 0.833333
221 YLA 0.413223 0.719101
222 K2K 0.412844 0.807692
223 8Q2 0.411765 0.663158
224 KYB 0.411215 0.777778
225 A3R 0.411215 0.709302
226 ADQ 0.411215 0.694118
227 KMQ 0.410714 0.72619
228 48N 0.410256 0.72093
229 0XU 0.41 0.824324
230 GA7 0.408696 0.72619
231 K3H 0.40708 0.775
232 7D3 0.40625 0.643678
233 PAP 0.405941 0.678571
234 DQV 0.405172 0.702381
235 OVE 0.404255 0.662791
236 4UV 0.403509 0.697674
237 ALF ADP 3PG 0.403361 0.712644
238 AF3 ADP 3PG 0.403361 0.712644
239 Q2P 0.403226 0.802469
240 3AD 0.402299 0.783784
241 2BA 0.402062 0.682927
242 CMP 0.402062 0.691358
243 K38 0.401786 0.7375
244 NAD TDB 0.4 0.731707
245 7C5 0.4 0.731707
246 NAD IBO 0.4 0.731707
Similar Ligands (3D)
Ligand no: 1; Ligand: MD0; Similar ligands found: 187
No: Ligand Similarity coefficient
1 MED 0.9522
2 ORN 0.9487
3 MEV 0.9435
4 MET 0.9345
5 DGL 0.9327
6 SRT 0.9314
7 DMV 0.9289
8 EHM 0.9284
9 MRY 0.9282
10 DLY 0.9265
11 RBL 0.9253
12 TLA 0.9252
13 LYS 0.9252
14 GLU 0.9249
15 IXW 0.9248
16 PAF 0.9212
17 GLN 0.9205
18 K6V 0.9202
19 PSJ 0.9197
20 9X7 0.9187
21 ASN 0.9185
22 FOC 0.9184
23 TZE 0.9165
24 AKG 0.9164
25 N6C 0.9158
26 QDK 0.9156
27 NLE 0.9137
28 IFL 0.9134
29 DMJ 0.9122
30 98J 0.9119
31 TAR 0.9108
32 ROR 0.9095
33 9J3 0.9094
34 COI 0.9093
35 NMH 0.9083
36 MLT 0.9075
37 KMT 0.9075
38 PZI 0.9069
39 VAH 0.9066
40 SKG 0.9063
41 ASP 0.9062
42 AL0 0.9051
43 ONL 0.9046
44 PEL 0.9043
45 OAA 0.9041
46 DGN 0.9038
47 2IT 0.9036
48 HSE 0.9035
49 LYN 0.9032
50 OPE 0.9014
51 MSE 0.9010
52 9ON 0.9004
53 PEP 0.9000
54 XLS 0.8993
55 RB0 0.8989
56 PAH 0.8989
57 IOM 0.8987
58 DPF 0.8986
59 Q07 0.8985
60 2CO 0.8975
61 GGL 0.8971
62 XYL 0.8967
63 RB5 0.8967
64 5FX 0.8967
65 XUL 0.8959
66 KOJ 0.8950
67 ZXD 0.8946
68 51F 0.8943
69 LMR 0.8943
70 MNM 0.8942
71 HY1 0.8940
72 URQ 0.8936
73 URP 0.8932
74 11C 0.8928
75 ONH 0.8925
76 7C3 0.8924
77 HCS 0.8922
78 6NA 0.8919
79 6JN 0.8919
80 8EW 0.8916
81 ZGL 0.8914
82 RUU 0.8913
83 CRN 0.8911
84 NVA 0.8910
85 3PG 0.8909
86 I38 0.8907
87 AOS 0.8906
88 49F 0.8905
89 ITN 0.8902
90 8GL 0.8901
91 I2M 0.8899
92 8SZ 0.8898
93 SEP 0.8897
94 FSG 0.8890
95 DHI 0.8885
96 HTX 0.8880
97 HDA 0.8879
98 A3M 0.8877
99 4SD 0.8877
100 GUA 0.8875
101 DZA 0.8871
102 GXL 0.8865
103 PCA 0.8863
104 2HG 0.8862
105 3HG 0.8861
106 2FT 0.8860
107 RIB 0.8855
108 SSB 0.8852
109 DIG 0.8851
110 HIS 0.8845
111 GLY ALA 0.8844
112 DTU 0.8843
113 LER 0.8836
114 9YT 0.8834
115 S2G 0.8831
116 FAN 0.8831
117 9X6 0.8824
118 NLP 0.8821
119 DAL DAL 0.8810
120 RNS 0.8808
121 4RW 0.8808
122 HYA 0.8807
123 C5A 0.8805
124 PGH 0.8802
125 DPJ 0.8802
126 HL5 0.8802
127 PLU 0.8801
128 TEO 0.8799
129 ALA ALA 0.8798
130 SYM 0.8794
131 DAS 0.8791
132 13P 0.8790
133 SR1 0.8786
134 IFM 0.8783
135 4XR 0.8777
136 LNO 0.8771
137 ARW 0.8761
138 ACA 0.8756
139 G4D 0.8755
140 CMS 0.8748
141 2EH 0.8748
142 3S5 0.8738
143 23W 0.8729
144 GLY PRO 0.8720
145 5XB 0.8719
146 CSS 0.8716
147 ICF 0.8715
148 4CS 0.8712
149 32O 0.8706
150 KMH 0.8705
151 SOR 0.8703
152 H76 0.8690
153 JZ7 0.8689
154 3OL 0.8679
155 DII 0.8674
156 OSE 0.8671
157 XBT 0.8665
158 2RH 0.8661
159 AE3 0.8661
160 GLO 0.8660
161 HL4 0.8656
162 N7P 0.8654
163 SHV 0.8650
164 MPJ 0.8646
165 PG0 0.8645
166 SLZ 0.8645
167 34V 0.8644
168 9YL 0.8636
169 DHS 0.8634
170 BAE 0.8631
171 ODV 0.8630
172 OKG 0.8626
173 ACH 0.8625
174 GP9 0.8624
175 SPD 0.8619
176 Q9Z 0.8614
177 IHG 0.8609
178 95Z 0.8598
179 1SH 0.8594
180 PSV 0.8592
181 TPO 0.8587
182 CCE 0.8574
183 OOG 0.8570
184 AFR 0.8547
185 FPK 0.8545
186 RAT 0.8543
187 A20 0.8517
Ligand no: 2; Ligand: SAM; Similar ligands found: 26
No: Ligand Similarity coefficient
1 TT8 0.9650
2 GDP 0.9145
3 8OD 0.9006
4 NWZ 0.8954
5 IDP 0.8910
6 CUU 0.8833
7 GNH 0.8826
8 KB7 0.8802
9 DTP 0.8779
10 GDP MG 0.8767
11 M7G 0.8755
12 G8D 0.8722
13 DZ4 0.8710
14 GTP 0.8703
15 DAT 0.8676
16 DGT 0.8665
17 GNP 0.8658
18 AV2 0.8650
19 HF7 0.8632
20 DGI 0.8627
21 HDV 0.8586
22 GCP 0.8586
23 TTP 0.8585
24 FZT 0.8567
25 GSP 0.8566
26 CTP 0.8538
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3T7V; Ligand: SAM; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3t7v.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3T7V; Ligand: MD0; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3t7v.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
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