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Receptor
PDB id Resolution Class Description Source Keywords
1U1J 2.4 Å EC: 2.1.1.14 A. THALIANA COBALAMINE INDEPENDENT METHIONINE SYNTHASE ARABIDOPSIS THALIANA METHIONINE SYNTHASE HOMOCYSTEINE METHYLTETRAHYDROFOLATE TRANSFERASE
Ref.: CRYSTAL STRUCTURES OF COBALAMIN-INDEPENDENT METHIONINE SYNTHASE COMPLEXED WITH ZINC, HOMOCYSTEINE, AND METHYLTETRAHYDROFOLATE J.BIOL.CHEM. V. 279 44235 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
C2F A:773;
Valid;
none;
submit data
459.456 C20 H25 N7 O6 C[N@@...
MET A:772;
Valid;
none;
submit data
149.211 C5 H11 N O2 S CSCC[...
SO4 A:768;
A:769;
A:770;
A:771;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
ZN A:766;
A:767;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1U1J 2.4 Å EC: 2.1.1.14 A. THALIANA COBALAMINE INDEPENDENT METHIONINE SYNTHASE ARABIDOPSIS THALIANA METHIONINE SYNTHASE HOMOCYSTEINE METHYLTETRAHYDROFOLATE TRANSFERASE
Ref.: CRYSTAL STRUCTURES OF COBALAMIN-INDEPENDENT METHIONINE SYNTHASE COMPLEXED WITH ZINC, HOMOCYSTEINE, AND METHYLTETRAHYDROFOLATE J.BIOL.CHEM. V. 279 44235 2004
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1U1J - MET C5 H11 N O2 S CSCC[C@@H]....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1U1J - MET C5 H11 N O2 S CSCC[C@@H]....
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1U1J - MET C5 H11 N O2 S CSCC[C@@H]....
2 4L6H ic50 = 4 mM MTX C20 H22 N8 O5 CN(Cc1cnc2....
3 4L61 - MET C5 H11 N O2 S CSCC[C@@H]....
4 4L64 - C2F C20 H25 N7 O6 C[N@@]1[C@....
5 4L5Z - HCS C4 H9 N O2 S C(CS)[C@@H....
6 4L6O - GLN C5 H10 N2 O3 C(CC(=O)N)....
7 4L65 - MET C5 H11 N O2 S CSCC[C@@H]....
8 1XDJ - HCS C4 H9 N O2 S C(CS)[C@@H....
9 3BQ5 - HCS C4 H9 N O2 S C(CS)[C@@H....
10 1XR2 - MRY C4 H10 O4 C([C@H]([C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: C2F; Similar ligands found: 27
No: Ligand ECFP6 Tc MDL keys Tc
1 C2F 1 1
2 FFO 0.739583 0.957747
3 TLL 0.635514 0.972603
4 THG 0.623762 0.887324
5 1YJ 0.623762 0.887324
6 THH 0.571429 0.84
7 MEF 0.555556 0.848101
8 FON 0.550459 0.957747
9 THF 0.509091 0.905405
10 1YA 0.486726 0.929577
11 9L9 0.460784 0.819444
12 3TZ 0.456897 0.696203
13 DHF 0.454545 0.887324
14 GHC 0.446429 0.658537
15 DZF 0.446429 0.756757
16 29C 0.444444 0.75
17 29D 0.444444 0.75
18 28Z 0.444444 0.75
19 83A 0.442478 0.74026
20 GHW 0.428571 0.666667
21 FOL 0.421053 0.77027
22 MHF 0.420168 0.848101
23 LYA 0.414414 0.701299
24 NHS 0.40708 0.712329
25 DDF 0.405172 0.813333
26 21V 0.405172 0.813333
27 TMF 0.403361 0.833333
Ligand no: 2; Ligand: MET; Similar ligands found: 32
No: Ligand ECFP6 Tc MDL keys Tc
1 MED 1 1
2 MET 1 1
3 DBB 0.518519 0.655172
4 ABA 0.518519 0.655172
5 2FM 0.514286 0.666667
6 MF3 0.5 0.647059
7 NVA 0.5 0.758621
8 HSE 0.466667 0.617647
9 DAB 0.466667 0.636364
10 MHO 0.457143 0.717949
11 SME 0.457143 0.717949
12 HCS 0.451613 0.733333
13 API 0.451613 0.606061
14 CDT 0.447368 0.756757
15 2MM 0.444444 0.657143
16 NLE 0.441176 0.766667
17 ONL 0.441176 0.71875
18 UN1 0.428571 0.606061
19 11C 0.428571 0.606061
20 MSE 0.428571 0.9
21 DGL 0.424242 0.625
22 GGL 0.424242 0.625
23 GLU 0.424242 0.625
24 CBH 0.418605 0.685714
25 ORN 0.411765 0.65625
26 FME 0.410256 0.84375
27 AME 0.410256 0.771429
28 LEU 0.40625 0.666667
29 JM6 0.4 0.7
30 CYS 0.4 0.666667
31 DCY 0.4 0.666667
32 C2N 0.4 0.633333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1U1J; Ligand: MET; Similar sites found with APoc: 178
This union binding pocket(no: 1) in the query (biounit: 1u1j.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 4PNI KQQ 1.06952
2 4M3P HCS 1.23153
3 4QTB 38Z 1.57895
4 3LOO B4P 1.64384
5 3PC3 P1T 1.70778
6 4A1O JLN 1.72084
7 3A1C ACP 1.74216
8 4A0S NAP 1.78971
9 2VRQ XYP XYP AHR 1.81452
10 1D6S MET PLP 1.86335
11 3FJO FMN 1.88383
12 3NC9 TR3 1.91693
13 4GNI ATP 1.95599
14 5EXW 7DT 2
15 4CTA ATP 2.03046
16 3VC3 C6P 2.03488
17 4Z87 5GP 2.09524
18 4M26 AKG 2.1978
19 4AOA IK2 2.20264
20 1PZO CBT 2.28137
21 6ASY ATP 2.31023
22 1S7G NAD 2.37154
23 1YP4 ADP 2.43902
24 1YP4 ADQ 2.43902
25 5N5S NAP 2.52427
26 1M7Y PPG 2.52874
27 1O68 KIV 2.54545
28 5X68 FAD 2.55754
29 4Q3S X7A 2.5974
30 1JXZ BCA 2.60223
31 4ZSY RW2 2.60304
32 1M3U KPL 2.65152
33 2R14 TXD 2.65252
34 2R14 FMN 2.65252
35 2J4K U5P 2.65487
36 5FB3 NDP 2.66272
37 4Z0G 5GP 2.66344
38 4GKV NAD 2.67857
39 1D1T NAD 2.68097
40 3V8S 0HD 2.68293
41 5MW4 5JU 2.69461
42 2PVF ACP 2.69461
43 2IXB A2G 2.7027
44 4ZVV NAD 2.71084
45 4ZVV GN0 2.71084
46 1XVA SAM 2.73973
47 2GND MAN MMA 2.77778
48 2PHF MAN MAN 2.77778
49 2AUY NAG MAN MMA 2.77778
50 2PHR MAN MAN 2.77778
51 2PHW MAN MAN 2.77778
52 2PHR MAN MAN BMA MAN 2.77778
53 2PHT MAN MAN MAN BMA MAN 2.77778
54 2AR6 NAG MAN 2.77778
55 2PHF MAN MAN BMA MAN 2.77778
56 1Q8P MAN MMA 2.77778
57 2PHX MAN MAN MAN MAN 2.77778
58 1Q8V MAN MAN MAN 2.77778
59 2AR6 NAG MAN MAN MAN NAG 2.77778
60 2PHU MAN MAN MAN BMA MAN 2.77778
61 1Q1R FAD 2.78422
62 2ZCQ B65 3.07167
63 5W8Q BU4 3.07692
64 1X1T NAD 3.07692
65 5B3A 0JO 3.08483
66 4J4H NAI 3.0888
67 4J4H 1J1 3.0888
68 5WO4 B7V 3.31126
69 2WKQ GTP 3.31325
70 3E5A VX6 3.35821
71 5DEY 59T 3.367
72 2C6Q NDP 3.4188
73 1M5B BN1 3.42205
74 1VLJ NAP 3.4398
75 3VEH 0GA 3.54767
76 1VYP TNF 3.57143
77 3HQP ATP 3.60721
78 4H2D FMN 3.63636
79 4I54 1C1 3.68272
80 3ENG CBI 3.75587
81 2G50 PYR 3.77358
82 5H5O PCG 3.87597
83 5EJ2 NAD 3.8961
84 3CTL S6P 3.8961
85 5GOO FRU 3.90456
86 3UZO GLU 3.91061
87 4KBA 1QM 3.92749
88 1Z0S ATP 3.95683
89 1PVN MZP 3.98936
90 1WUU ANP 4.01003
91 5B2E MQG 4.04412
92 5UKL SIX 4.12979
93 2VVT I24 4.13793
94 2ZJF BSU 4.14365
95 2I80 G1L 4.16667
96 1PS9 FMN 4.17288
97 6C2Z P1T 4.26667
98 2PZI AXX 4.31373
99 5JCM FAD 4.43459
100 5JCM ISD 4.43459
101 5JCM NAD 4.43459
102 5FI3 NAP 4.48179
103 3TLJ SAH 4.55764
104 4USF 6UI 4.60526
105 3BZ3 YAM 4.71014
106 1NZY BCA 4.83271
107 5YVR NDP 4.88998
108 5I7Y 69G 4.9505
109 5MZI FYK 4.98915
110 5MZI FAD 4.98915
111 3N39 FMN 5.22876
112 3X44 PUS 5.42169
113 2VAR ANP 5.43131
114 2I6A 5I5 5.50725
115 3MQG ACO 5.72917
116 4MZU COA 5.76923
117 3ZCN ATP 5.82011
118 3DLS ADP 5.97015
119 4ZDC CO8 6
120 6FHO FAD 6.01504
121 5XWV 8H6 6.04839
122 5M3E APR 6.06061
123 2JDU MFU 6.08696
124 2CVQ NDP 6.11621
125 5THZ SAH 6.17284
126 5O4J PJL 6.20438
127 5O4J 9KH 6.20438
128 5O4J SAH 6.20438
129 3IE3 N11 6.2201
130 1GSA GSH 6.32911
131 2YVJ FAD 6.42202
132 3OVR 5SP 6.57895
133 4B9Q ATP 6.61157
134 2CHG ANP 6.63717
135 5TC4 L34 6.64557
136 1H70 CIR 6.66667
137 4Q3R XA2 6.75325
138 2AEB ABH 6.8323
139 3ZYR ASN NAG NAG BMA MAN MAN NAG NAG 6.89655
140 4Y7U 2KH 6.92641
141 2FB3 MET 7.05882
142 2FB3 GTP 7.05882
143 2FB3 5AD 7.05882
144 1KEV NDP 7.12251
145 4E2J MOF 7.2
146 2VSS ACO 7.24638
147 2VSU ACO 7.27273
148 5EYY MDM 7.34694
149 2YK7 CSF 7.36196
150 3C0G 3AM 7.69231
151 2GSD NAD 7.71144
152 1VBH PEP 7.71242
153 2V2V V12 7.74908
154 1OIV GDP 7.8534
155 6FOG OXL 8.03571
156 4O6M C5P 8.06452
157 3T64 DU3 8.28729
158 2BPM 529 8.30189
159 5HQ0 LZ9 8.33333
160 5BO9 SIA GAL NGS 8.66873
161 4NG2 OHN 8.84956
162 4J36 FAD 8.91566
163 4J36 1HR 8.91566
164 4XIZ LPP 10
165 3SAO NKN 10
166 4M20 COA 10.2362
167 4F9C 0SX 10.8033
168 1O97 AMP 11.3636
169 2AZ5 307 11.4865
170 2CJF RP4 12.1019
171 3HUJ AGH 15.1515
172 3LXK MI1 15.2905
173 2FLI DX5 15.9091
174 1XVB BHL 18.2353
175 5YYF PHQ GLN THR ALA ARG LYS NH2 FOA 19.8582
176 4QAR ADE 25.8706
177 2D1K ATP 28.125
178 4GUS FAD 29.8387
Pocket No.: 2; Query (leader) PDB : 1U1J; Ligand: C2F; Similar sites found with APoc: 27
This union binding pocket(no: 2) in the query (biounit: 1u1j.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 5ZQS XYP 1.66359
2 3HKW IX6 1.72117
3 4MIB 28M 1.92982
4 5U61 7WG 2.07612
5 2I7C AAT 2.4735
6 5TTJ FAD 2.85714
7 3K7M FAD 3.48028
8 4DS0 A2G GAL NAG FUC 3.68098
9 3AB4 LYS 3.93258
10 1U1B PAX 4.03226
11 3HCH RSM 4.10959
12 1K4M NAD 4.22535
13 5FVJ ACO 7.22892
14 5UBG PRT 7.52212
15 1LO8 4CA 8.51064
16 5WXH ALA ARG THR M3L GLN THR ALA 9.52381
17 2VNF ALA ARG THR M3L GLN THR ALA ARG LYS SER 10
18 2H29 DND 11.1111
19 1RZX ACE VAL LYS GLU SER LEU VAL 11.2245
20 2J9D ADP 11.7647
21 5ULP KB1 11.9403
22 1MFG GLU TYR LEU GLY LEU ASP VAL PRO VAL 14.7368
23 4CO3 ATP 22.3214
24 5VWK PRO ALA TRP ASP GLU THR ASN LEU 24.5902
25 4GUT FAD 29.8387
26 4GUS FAD 29.8387
27 4HSU FAD 29.8387
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