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
Ligand no: 1; Ligand: MD0; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 MD0 1 1
2 ILE 0.551724 0.655172
3 DAB 0.466667 0.827586
Ligand no: 2; Ligand: SAM; Similar ligands found: 192
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 XYA 0.565789 0.773333
9 ADN 0.565789 0.773333
10 RAB 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 DTA 0.536585 0.789474
21 62X 0.535354 0.884615
22 MTA 0.53012 0.875
23 3DH 0.517647 0.849315
24 AMP MG 0.511364 0.710843
25 5AL 0.510417 0.743902
26 VMS 0.510204 0.673913
27 54H 0.510204 0.673913
28 0UM 0.51 0.857143
29 A 0.505747 0.707317
30 AMP 0.505747 0.707317
31 ABM 0.505618 0.753086
32 A5A 0.505155 0.688889
33 DAL AMP 0.50505 0.765432
34 NVA LMS 0.504951 0.725275
35 K15 0.5 0.883117
36 6RE 0.5 0.78481
37 5AD 0.5 0.75
38 SSA 0.5 0.684783
39 SON 0.5 0.746988
40 SRP 0.5 0.746988
41 LSS 0.49505 0.706522
42 CA0 0.494624 0.714286
43 A12 0.494505 0.705882
44 AP2 0.494505 0.705882
45 ME8 0.490385 0.841463
46 5CA 0.49 0.684783
47 TSB 0.49 0.681319
48 53H 0.49 0.666667
49 ACP 0.489362 0.694118
50 5AS 0.48913 0.648936
51 ADP 0.48913 0.690476
52 A2D 0.488889 0.690476
53 J7C 0.488889 0.772152
54 ZAS 0.488636 0.769231
55 8QN 0.485149 0.743902
56 GAP 0.484536 0.73494
57 AN2 0.483871 0.682353
58 A3S 0.483871 0.813333
59 A7D 0.483871 0.851351
60 GJV 0.483516 0.775
61 SRA 0.483146 0.694118
62 LAD 0.480769 0.752941
63 KAA 0.480769 0.698925
64 GSU 0.480769 0.722222
65 AMO 0.480392 0.746988
66 DSZ 0.480392 0.703297
67 52H 0.48 0.666667
68 ADP MG 0.478723 0.702381
69 M33 0.478723 0.722892
70 MAO 0.478261 0.82716
71 BA3 0.478261 0.690476
72 AOC 0.477778 0.776316
73 DSH 0.477778 0.842105
74 NEC 0.477778 0.75
75 SXZ 0.47619 0.894737
76 AHX 0.475728 0.701149
77 Y3J 0.47561 0.706667
78 G5A 0.474227 0.684783
79 A3T 0.473684 0.8
80 ADP BEF 0.473684 0.686047
81 BEF ADP 0.473684 0.686047
82 B4P 0.473118 0.690476
83 AP5 0.473118 0.690476
84 A3N 0.472527 0.766234
85 KB1 0.471698 0.833333
86 LEU LMS 0.471154 0.706522
87 APC 0.46875 0.705882
88 PRX 0.46875 0.73494
89 PAJ 0.466019 0.712644
90 4AD 0.466019 0.759036
91 RBY 0.463918 0.72619
92 ADP PO3 0.463918 0.728395
93 ADV 0.463918 0.72619
94 ADX 0.463158 0.666667
95 MHZ 0.463158 0.82716
96 AU1 0.463158 0.674419
97 YAP 0.462963 0.738095
98 TXA 0.462264 0.72619
99 NB8 0.462264 0.72093
100 A3G 0.461538 0.802632
101 VRT 0.459184 0.842105
102 ATP MG 0.459184 0.702381
103 YSA 0.458716 0.684783
104 XAH 0.458716 0.715909
105 50T 0.458333 0.682353
106 ATP 0.458333 0.690476
107 7D7 0.45679 0.723684
108 ANP MG 0.455446 0.678161
109 KH3 0.455357 0.871795
110 ACQ 0.454545 0.694118
111 AQP 0.453608 0.690476
112 5FA 0.453608 0.690476
113 AR6 0.453608 0.710843
114 APR 0.453608 0.710843
115 NSS 0.451923 0.703297
116 FA5 0.449541 0.746988
117 AGS 0.44898 0.678161
118 SAP 0.44898 0.678161
119 A5D 0.44898 0.789474
120 AD9 0.44898 0.674419
121 PTJ 0.448598 0.72093
122 YLB 0.448276 0.758621
123 YLP 0.447368 0.738636
124 D3Y 0.446602 0.792208
125 ADP ALF 0.445545 0.678161
126 ALF ADP 0.445545 0.678161
127 TYR AMP 0.445455 0.746988
128 MYR AMP 0.444444 0.776471
129 3AM 0.444444 0.674699
130 OAD 0.443396 0.73494
131 2VA 0.443299 0.779221
132 OOB 0.442308 0.722892
133 S8M 0.442308 0.831169
134 ADP VO4 0.441176 0.702381
135 VO4 ADP 0.441176 0.702381
136 ANP 0.44 0.674419
137 TAT 0.44 0.686047
138 WAQ 0.439252 0.75
139 ARG AMP 0.438596 0.727273
140 YLC 0.435897 0.755814
141 AAT 0.435644 0.797468
142 3OD 0.435185 0.73494
143 1ZZ 0.435185 0.755814
144 NVA 2AD 0.434343 0.815789
145 DLL 0.433962 0.722892
146 00A 0.433962 0.689655
147 7MD 0.433628 0.715909
148 ATF 0.431373 0.666667
149 SO8 0.43 0.792208
150 3UK 0.429907 0.714286
151 A6D 0.429907 0.72619
152 5SV 0.428571 0.741176
153 AMP DBH 0.428571 0.714286
154 WSA 0.42735 0.692308
155 TYM 0.42735 0.746988
156 9SN 0.427273 0.681818
157 AHZ 0.426087 0.755814
158 A A 0.425926 0.710843
159 3NZ 0.425926 0.807692
160 P5A 0.425926 0.691489
161 PR8 0.425926 0.744186
162 A1R 0.424528 0.709302
163 2A5 0.424242 0.674419
164 7MC 0.423729 0.719101
165 7D5 0.422222 0.658824
166 FYA 0.422018 0.722892
167 JB6 0.422018 0.709302
168 AYB 0.421488 0.75
169 PLP AAD 0.419355 0.764045
170 A22 0.419048 0.682353
171 MAP 0.419048 0.659091
172 2AM 0.417582 0.666667
173 TAD 0.417391 0.712644
174 A3P 0.416667 0.686747
175 ADP BMA 0.416667 0.714286
176 25A 0.415094 0.690476
177 YLA 0.413223 0.719101
178 ADQ 0.411215 0.694118
179 48N 0.410256 0.72093
180 0XU 0.41 0.824324
181 NAD IBO 0.406504 0.717647
182 7D3 0.40625 0.643678
183 PAP 0.405941 0.678571
184 OVE 0.404255 0.662791
185 4UV 0.403509 0.697674
186 ALF ADP 3PG 0.403361 0.712644
187 AF3 ADP 3PG 0.403361 0.712644
188 LA8 ALF 3PG 0.403361 0.712644
189 3AD 0.402299 0.783784
190 CMP 0.402062 0.691358
191 2BA 0.402062 0.682927
192 7C5 0.4 0.731707
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3T7V; Ligand: SAM; Similar sites found: 34
This union binding pocket(no: 1) in the query (biounit: 3t7v.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4CQK PIO 0.02889 0.40609 None
2 4FHD EEM 0.01117 0.40173 2.71739
3 4FHD 0TT 0.01117 0.40173 2.71739
4 1YQC GLV 0.007056 0.42599 2.94118
5 3VSV XYS 0.016 0.41952 4
6 1O9U ADZ 0.006969 0.44995 4.28571
7 3RFA SAM 0.0003874 0.43685 4.28571
8 3ANY 2A3 0.01665 0.41044 4.57143
9 4ZGR NGA GAL 0.03466 0.40204 5.66802
10 4GYI ADP 0.003728 0.43177 6
11 4UWH JXM 0.003695 0.42761 6
12 5WGG SAM 0.0008842 0.4517 6.28571
13 4LH7 1X8 0.009222 0.43372 6.50155
14 5UL4 SAM 0.0002367 0.43663 8.57143
15 2FB3 GTP 0.002143 0.43029 10
16 2FB3 5AD 0.0004118 0.42842 10
17 2FB3 MET 0.0003526 0.42348 10
18 3AB4 THR 0.0181 0.40685 10.6742
19 1KTG AMP 0.02645 0.40571 12.3188
20 3LQV ADE 0.02546 0.40503 12.8205
21 4K37 SAM 0.00006712 0.50251 15.4286
22 4K38 SAM 0.0000662 0.47054 15.4286
23 4K39 SAM 0.0001263 0.45258 15.4286
24 4WCX SAM 0.0000006205 0.56633 15.7143
25 4WCX MET 0.0003768 0.49686 15.7143
26 5VSM MET 0.0001741 0.46882 19.1824
27 5VSM 5AD 0.0001844 0.46775 19.1824
28 4LO2 GAL BGC 0.02108 0.41545 19.9324
29 5EXK 5AD 0.000005068 0.44436 20.5438
30 1OLT SAM 0.00001763 0.51675 23.1429
31 4R33 TRP 0.0000002126 0.61156 23.7143
32 4R33 SAH 0.0000002126 0.61156 23.7143
33 4U0O MTA 0.0001277 0.46099 23.9865
34 4JYD SAH 0.000000006749 0.56616 45.6897
Pocket No.: 2; Query (leader) PDB : 3T7V; Ligand: MD0; Similar sites found: 67
This union binding pocket(no: 2) in the query (biounit: 3t7v.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3SAO NKN 0.01271 0.4051 1.25
2 4IP7 FLC 0.003438 0.42753 1.71429
3 4KCT PYR 0.0053 0.41044 2
4 1GQG DCD 0.007121 0.43377 2.57143
5 1ZOA 140 0.01886 0.42709 2.57143
6 3UXL CFI 0.03384 0.41793 2.57143
7 3HQP OXL 0.02736 0.40186 2.57143
8 2WQP WQP 0.01482 0.42317 2.5788
9 3BU1 HSM 0.005581 0.42554 2.7027
10 1RWQ 5AP 0.0463 0.40672 2.85714
11 2C49 ADN 0.006783 0.42754 2.98013
12 3EPO MP5 0.001077 0.47012 3.14286
13 2ZX7 ZX7 0.02331 0.4021 3.14286
14 3MKN DNB 0.01437 0.40902 3.16456
15 1ZB6 GST 0.01903 0.42003 3.25733
16 1ZB6 DIN 0.02437 0.41304 3.25733
17 2Y88 2ER 0.04291 0.40757 3.27869
18 3HQR OGA 0.01668 0.40154 3.65854
19 2YCJ C2F 0.01394 0.40763 3.69004
20 1M6P M6P 0.002264 0.43633 3.94737
21 1TB3 FMN 0.02712 0.41301 4
22 1Q23 FUA 0.01488 0.41386 4.10959
23 5XSS XYP 0.01102 0.40296 4.11392
24 1M3U KPL 0.0006324 0.45329 4.16667
25 3OJI PYV 0.01713 0.41072 4.2328
26 3FYP PEP 0.002301 0.42703 4.28571
27 4Z1D PEP 0.007629 0.41144 4.34783
28 5I8F ML1 0.01153 0.40719 4.84848
29 4L6H HCS 0.003163 0.43218 4.85714
30 1I06 TZL 0.002858 0.43142 5
31 2OAZ I96 0.02654 0.40255 5.14286
32 2RDT 2RD 0.02945 0.41224 6
33 2B82 ADN 0.003742 0.44643 6.16114
34 3IU9 T07 0.02074 0.42686 6.25
35 2NLI FMN 0.03228 0.40525 6.28571
36 3G6K FAD 0.04426 0.40375 6.81818
37 3G6K POP 0.04028 0.40375 6.81818
38 1REQ DCA 0.03923 0.41606 6.85714
39 3AGC RCC 0.008757 0.43521 6.88406
40 3BEJ MUF 0.009118 0.42821 7.56302
41 1Y0G 8PP 0.03858 0.41562 7.8534
42 1QPR PPC 0.01228 0.41988 8.4507
43 2V63 CAP 0.006788 0.43313 8.57143
44 2VDH CAP 0.006815 0.43304 8.57143
45 3B1Q NOS 0.01652 0.40977 8.58896
46 2GPT TLA 0.006165 0.41799 9.14286
47 5D6T NGA 0.004763 0.40618 9.92647
48 5JNN 6LM 0.01166 0.42427 10
49 1R87 XYP XYP XYP 0.01947 0.40428 10.2857
50 1GYM MYG 0.0001224 0.44036 10.4027
51 3EXS 5RP 0.004666 0.40673 10.8597
52 1KBJ FMN 0.01217 0.42628 11.1429
53 2TPS TPS 0.003769 0.45295 11.4537
54 3H22 B53 0.002684 0.43842 12.4579
55 1OFD FMN 0.02508 0.42035 12.5714
56 1OFD AKG 0.04238 0.40583 12.5714
57 5A5W GUO 0.008439 0.4502 12.6482
58 1GZW GAL BGC 0.008097 0.4019 13.4328
59 1QXW M1C 0.002447 0.45202 13.8889
60 1UZD CAP 0.007406 0.43119 14.1791
61 4OIC A8S 0.0141 0.40945 15.4589
62 4A8H PUW 0.01092 0.41896 15.7746
63 1JCM 137 0.01923 0.40456 19.305
64 5JSP DQY 0.0125 0.40223 21.393
65 2X32 OTP 0.04994 0.41254 23.4637
66 4R33 TRP 0.01557 0.42943 23.7143
67 4R33 SAH 0.01557 0.42943 23.7143
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