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 DZF 0.446429 0.756757
15 GHC 0.446429 0.658537
16 29D 0.444444 0.75
17 28Z 0.444444 0.75
18 29C 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 21V 0.405172 0.813333
26 DDF 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 MET 1 1
2 MED 1 1
3 DBB 0.518519 0.655172
4 ABA 0.518519 0.655172
5 2FM 0.514286 0.666667
6 NVA 0.5 0.758621
7 MF3 0.5 0.647059
8 DAB 0.466667 0.636364
9 HSE 0.466667 0.617647
10 SME 0.457143 0.717949
11 MHO 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 GGL 0.424242 0.625
22 GLU 0.424242 0.625
23 DGL 0.424242 0.625
24 CBH 0.418605 0.685714
25 ORN 0.411765 0.65625
26 AME 0.410256 0.771429
27 FME 0.410256 0.84375
28 LEU 0.40625 0.666667
29 CYS 0.4 0.666667
30 C2N 0.4 0.633333
31 DCY 0.4 0.666667
32 JM6 0.4 0.7
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1U1J; Ligand: MET; Similar sites found: 100
This union binding pocket(no: 1) in the query (biounit: 1u1j.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1KC7 PPR 0.003984 0.40503 1.30719
2 4QTB 38Z 0.03604 0.40171 1.57895
3 3LOO B4P 0.02938 0.41609 1.64384
4 4A1O JLN 0.03375 0.40453 1.72084
5 3A1C ACP 0.007568 0.42319 1.74216
6 1RYD GLC 0.01933 0.40266 1.80879
7 2VRQ XYP XYP AHR 0.01905 0.40013 1.81452
8 1D6S MET PLP 0.005676 0.4408 1.86335
9 3FJO FMN 0.0157 0.41293 1.88383
10 4GNI ATP 0.0197 0.40676 1.95599
11 5F1X ATP 0.02998 0.40303 2
12 4CTA ATP 0.009783 0.43398 2.03046
13 3VC3 C6P 0.008828 0.43299 2.03488
14 5MY8 RXZ 0.01624 0.41603 2.08877
15 4AOA IK2 0.008249 0.42322 2.20264
16 1S7G NAD 0.04066 0.41072 2.37154
17 1YP4 ADQ 0.007127 0.4429 2.43902
18 1M7Y PPG 0.02391 0.41099 2.52874
19 1JXZ BCA 0.01279 0.42771 2.60223
20 1D1T NAD 0.02939 0.41264 2.68097
21 3V8S 0HD 0.0169 0.40741 2.68293
22 5MW4 5JU 0.03078 0.41078 2.69461
23 1XVA SAM 0.0312 0.40798 2.73973
24 2PHF MAN MAN 0.003221 0.41929 2.77778
25 2AR6 NAG MAN 0.007634 0.4102 2.77778
26 2PHF MAN MAN BMA MAN 0.004883 0.41011 2.77778
27 1Q8P MAN MMA 0.004511 0.40959 2.77778
28 2PHX MAN MAN MAN MAN 0.004894 0.40862 2.77778
29 1Q8V MAN MAN MAN 0.005003 0.40759 2.77778
30 2AR6 NAG MAN MAN MAN NAG 0.01174 0.40371 2.77778
31 2PHU MAN MAN MAN BMA MAN 0.006706 0.40296 2.77778
32 2ZCQ B65 0.01951 0.42201 3.07167
33 5B3A 0JO 0.01855 0.41574 3.08483
34 4J4H NAI 0.01155 0.4409 3.0888
35 4J4H 1J1 0.01155 0.4409 3.0888
36 3VEH 0GA 0.007869 0.41598 3.54767
37 1VYP FMN 0.02477 0.40018 3.57143
38 1VYP TNF 0.02346 0.40018 3.57143
39 3HQP ATP 0.03442 0.4012 3.60721
40 2J7T 274 0.02479 0.43894 3.64238
41 3ENG CBI 0.01207 0.41155 3.75587
42 3CTL S6P 0.01774 0.40191 3.8961
43 1WUU ANP 0.01896 0.41937 4.01003
44 5B2E MQG 0.01735 0.40069 4.04412
45 5UKL SIX 0.01744 0.409 4.12979
46 2VVT I24 0.01864 0.42088 4.13793
47 2ZJF BSU 0.01154 0.41354 4.14365
48 1PS9 FMN 0.01968 0.40882 4.17288
49 2NW9 FT6 0.02323 0.40271 4.24837
50 2P41 SAH 0.03864 0.40969 4.2623
51 5JCM FAD 0.02418 0.43224 4.43459
52 5JCM ISD 0.02469 0.43224 4.43459
53 5JCM NAD 0.02469 0.43224 4.43459
54 4USF 6UI 0.008691 0.43627 4.60526
55 1NZY BCA 0.01604 0.42018 4.83271
56 5MZI FYK 0.02274 0.42592 4.98915
57 5MZI FAD 0.02223 0.42592 4.98915
58 3ZEU AGS 0.01925 0.40496 5.04451
59 3ZEU ADP 0.02027 0.40144 5.04451
60 3N39 FMN 0.01848 0.40843 5.22876
61 2VAR ANP 0.01681 0.40008 5.43131
62 2WQP WQP 0.03397 0.40637 5.44413
63 2I6A 5I5 0.01163 0.42154 5.50725
64 3DLS ADP 0.02911 0.40195 5.97015
65 5M3E APR 0.01196 0.43427 6.06061
66 1H82 GZZ 0.03737 0.44398 6.14407
67 1H82 FAD 0.03508 0.44398 6.14407
68 5THZ SAH 0.03041 0.40156 6.17284
69 5HES 032 0.01655 0.42095 6.18893
70 5O4J PJL 0.01357 0.42684 6.20438
71 5O4J SAH 0.01766 0.42012 6.20438
72 5O4J 9KH 0.01766 0.42012 6.20438
73 1GSA GSH 0.02778 0.40063 6.32911
74 4B9Q ATP 0.0338 0.40284 6.61157
75 2CHG ANP 0.02677 0.40337 6.63717
76 1H70 CIR 0.01132 0.41403 6.66667
77 2AEB ABH 0.0223 0.40105 6.8323
78 3ZYR ASN NAG NAG BMA MAN MAN NAG NAG 0.005881 0.42395 6.89655
79 4Y7U 2KH 0.03037 0.40676 6.92641
80 2FB3 GTP 0.04916 0.40175 7.05882
81 2FB3 MET 0.02194 0.40175 7.05882
82 2FB3 5AD 0.02391 0.40175 7.05882
83 2VSU ACO 0.02611 0.40247 7.27273
84 5IXJ THR 0.02133 0.42499 7.32323
85 2YK7 CSF 0.0237 0.40348 7.36196
86 3C0G 3AM 0.02938 0.40412 7.69231
87 1VBH PEP 0.006687 0.40537 7.71242
88 1OIV GDP 0.01643 0.42624 7.8534
89 4O6M C5P 0.01286 0.40418 8.06452
90 3T64 DU3 0.0228 0.40753 8.28729
91 5HQ0 LZ9 0.01383 0.40371 8.33333
92 5BO9 SIA GAL NGS 0.03677 0.41292 8.66873
93 4NG2 OHN 0.04003 0.40177 8.84956
94 4J36 FAD 0.01253 0.42219 8.91566
95 4J36 1HR 0.01995 0.41881 8.91566
96 1NXJ GLV 0.04396 0.4041 9.28962
97 4XIZ LPP 0.04494 0.40818 10
98 3SAO NKN 0.0169 0.40012 10
99 4F9C 0SX 0.01868 0.40505 10.8033
100 4QAR ADE 0.01135 0.40801 25.8706
Pocket No.: 2; Query (leader) PDB : 1U1J; Ligand: C2F; Similar sites found: 17
This union binding pocket(no: 2) in the query (biounit: 1u1j.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5TTJ FAD 0.02155 0.42777 2.85714
2 4WYU SER TRP PHE GLN THR ASP LEU 0.01823 0.40601 3.30189
3 4DS0 A2G GAL NAG FUC 0.006251 0.40896 3.68098
4 1U1B PAX 0.04249 0.40349 4.03226
5 1K4M NAD 0.02573 0.41525 4.22535
6 4TWP AXI 0.04432 0.42994 8.11808
7 1LO8 4CA 0.01475 0.43037 8.51064
8 2VNF ALA ARG THR M3L GLN THR ALA ARG LYS SER 0.001355 0.46544 10
9 5AYF C7H 0.01182 0.4385 11.0266
10 5AYF SAM 0.01074 0.4385 11.0266
11 2H29 DND 0.04189 0.40867 11.1111
12 1RZX ACE VAL LYS GLU SER LEU VAL 0.01137 0.40532 11.2245
13 2J9D ADP 0.01815 0.4145 11.7647
14 5ULP KB1 0.01313 0.42105 11.9403
15 4CO3 ATP 0.04183 0.40367 22.3214
16 4GUT FAD 0.04447 0.41405 29.8387
17 4HSU FAD 0.04795 0.41048 29.8387
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