Receptor
PDB id Resolution Class Description Source Keywords
3BOF 1.7 Å EC: 2.1.1.13 COBALAMIN-DEPENDENT METHIONINE SYNTHASE (1-566) FROM THERMOTOGA MARITIMA COMPLEXED WITH ZN2+ AND HOMOCYSTEINE THERMOTOGA MARITIMA METH TRANSFERASE TIM BARREL HOMOCYSTEINE ZINC ZINC INVERSION METHYLTRANSFERASE
Ref.: METAL ACTIVE SITE ELASTICITY LINKED TO ACTIVATION OF HOMOCYSTEINE IN METHIONINE SYNTHASES. PROC.NATL.ACAD.SCI.USA V. 105 3286 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
HCS A:711;
B:712;
Valid;
Valid;
none;
none;
submit data
135.185 C4 H9 N O2 S C(CS)...
K A:703;
B:704;
Part of Protein;
Part of Protein;
none;
none;
submit data
39.098 K [K+]
YT3 A:705;
Invalid;
none;
submit data
88.906 Y [Y+3]
ZN A:701;
B:702;
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
3BOF 1.7 Å EC: 2.1.1.13 COBALAMIN-DEPENDENT METHIONINE SYNTHASE (1-566) FROM THERMOTOGA MARITIMA COMPLEXED WITH ZN2+ AND HOMOCYSTEINE THERMOTOGA MARITIMA METH TRANSFERASE TIM BARREL HOMOCYSTEINE ZINC ZINC INVERSION METHYLTRANSFERASE
Ref.: METAL ACTIVE SITE ELASTICITY LINKED TO ACTIVATION OF HOMOCYSTEINE IN METHIONINE SYNTHASES. PROC.NATL.ACAD.SCI.USA V. 105 3286 2008
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3BOL - HCS C4 H9 N O2 S C(CS)[C@@H....
2 1Q8J - HCS C4 H9 N O2 S C(CS)[C@@H....
3 3BOF - HCS C4 H9 N O2 S C(CS)[C@@H....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3BOL - HCS C4 H9 N O2 S C(CS)[C@@H....
2 1Q8J - HCS C4 H9 N O2 S C(CS)[C@@H....
3 3BOF - HCS C4 H9 N O2 S C(CS)[C@@H....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3BOL - HCS C4 H9 N O2 S C(CS)[C@@H....
2 1Q8J - HCS C4 H9 N O2 S C(CS)[C@@H....
3 3BOF - HCS C4 H9 N O2 S C(CS)[C@@H....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: HCS; Similar ligands found: 45
No: Ligand ECFP6 Tc MDL keys Tc
1 HCS 1 1
2 CYS 0.608696 0.916667
3 DCY 0.608696 0.916667
4 DAB 0.56 0.851852
5 HSE 0.56 0.821429
6 GGL 0.555556 0.714286
7 GLU 0.555556 0.714286
8 DGL 0.555556 0.714286
9 NVA 0.538462 0.740741
10 API 0.538462 0.689655
11 DBB 0.5 0.692308
12 DSN 0.5 0.777778
13 DGN 0.5 0.645161
14 2RA 0.5 0.75
15 SER 0.5 0.777778
16 ABA 0.5 0.692308
17 GLN 0.5 0.645161
18 ORN 0.482759 0.814815
19 C2N 0.48 0.730769
20 ONL 0.466667 0.645161
21 NLE 0.466667 0.689655
22 CSS 0.464286 0.75
23 ASP 0.461538 0.655172
24 DAS 0.461538 0.655172
25 MET 0.451613 0.733333
26 MED 0.451613 0.733333
27 MSE 0.451613 0.65625
28 DLY 0.451613 0.785714
29 UN1 0.451613 0.689655
30 11C 0.451613 0.689655
31 DHH 0.4375 0.666667
32 LYS 0.4375 0.758621
33 KKA 0.428571 0.685714
34 LEU 0.428571 0.642857
35 CSO 0.428571 0.636364
36 AS2 0.428571 0.642857
37 NPI 0.424242 0.666667
38 ONH 0.424242 0.611111
39 6CL 0.411765 0.666667
40 26P 0.411765 0.625
41 2FM 0.411765 0.758621
42 3GC 0.410256 0.705882
43 VUR 0.410256 0.657143
44 CIR 0.4 0.611111
45 MF3 0.4 0.733333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3BOF; Ligand: HCS; Similar sites found: 56
This union binding pocket(no: 1) in the query (biounit: 3bof.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5EB4 FAD 0.04562 0.41169 1.69173
2 5JY4 ISC 0.008805 0.42272 1.79028
3 1CM8 ANP 0.01694 0.40548 1.90736
4 5KGS 6SR 0.03953 0.41792 1.96937
5 2WL5 COA 0.03186 0.40095 2.04082
6 2DKH 3HB 0.02151 0.42997 2.12014
7 4A2B AGS 0.007639 0.43265 2.38663
8 4A2A ATP 0.01875 0.40954 2.38663
9 1UNH IXM 0.01098 0.4125 2.40385
10 4GKV NAD 0.04898 0.40343 2.67857
11 5LXC 7AA 0.008383 0.4203 2.94118
12 5W10 CMP 0.01934 0.4078 3.07692
13 4ASE AV9 0.03352 0.40508 3.11615
14 1R37 NAD 0.007449 0.44823 3.17003
15 1CDO NAD 0.02933 0.40799 3.20856
16 4QTB 38Z 0.0105 0.43475 3.42105
17 1KOL NAD 0.03346 0.41594 3.51759
18 3KU0 ADE 0.008673 0.40901 3.58566
19 3BY9 SIN 0.003349 0.42752 3.84615
20 1NFQ NAI 0.03211 0.41196 3.84615
21 3E7O 35F 0.03564 0.40853 3.88889
22 2GCG DGY 0.001433 0.43651 3.93939
23 1FAO 4IP 0.01143 0.40541 3.96825
24 4L2I NAD 0.0269 0.42889 4.04624
25 3WLE NAD 0.008701 0.44782 4.39883
26 2VPQ ANP 0.02316 0.40848 4.43459
27 1UGY GLA BGC 0.00269 0.42052 4.51128
28 3MDV CL6 0.04571 0.40498 4.60526
29 2HK5 1BM 0.009799 0.42512 4.81482
30 1PHP ADP 0.02573 0.40614 4.82234
31 3TN7 NJP 0.0378 0.40646 5.05837
32 5L2Z 70C 0.02138 0.42461 5.17241
33 3O61 GDD 0.0166 0.41693 5.2356
34 2UVO NDG 0.004906 0.42149 5.26316
35 2UVO NAG 0.004906 0.42149 5.26316
36 5VZ0 ADP 0.01115 0.4167 5.30035
37 3ZRM ZRM 0.013 0.41393 5.39084
38 5B4B LP5 0.04565 0.40111 5.64516
39 4U0I 0LI 0.01679 0.42541 5.71429
40 4YJK URA 0.01254 0.40359 5.95238
41 4LUT DCS 0.01915 0.40713 5.97403
42 4CQM NAP 0.02155 0.41961 6.51341
43 3LLZ GAL NGA 0.009102 0.40708 6.76692
44 3NZ1 3NY 0.01094 0.4058 6.89655
45 2OO8 RAJ 0.01083 0.42415 7.88644
46 3OFM 4B0 0.01856 0.40064 8
47 2WSB NAD 0.02693 0.42484 8.26772
48 4F9C 0SX 0.02146 0.40145 8.33333
49 4P42 PEE 0.03424 0.40352 8.64979
50 1EYQ NAR 0.01111 0.40785 9.90991
51 2WEL K88 0.002025 0.43787 10
52 1YY5 FAD 0.03792 0.41899 10.3314
53 4XB4 45D 0.02186 0.41041 26.3158
54 3TYZ PAB 0.03379 0.40449 27.8571
55 4M3P HCS 0.00000006874 0.69533 31.7734
56 5DMM HCS 0.0000006671 0.62087 41.6129
Pocket No.: 2; Query (leader) PDB : 3BOF; Ligand: HCS; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3bof.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Feedback