Receptor
PDB id Resolution Class Description Source Keywords
5VYQ 1.6 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE N-FORMYLTRANSFERASE RV3404C FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH YDP-QUI4N AND FO MYCOBACTERIUM TUBERCULOSIS CAS/NITR204ORGANISM_TAXID: 1310114 FORMYLTRANSFERASE DEOXYSUGAR TRANSFERASE
Ref.: BIOCHEMICAL INVESTIGATION OF RV3404C FROM MYCOBACTE TUBERCULOSIS. BIOCHEMISTRY V. 56 3818 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
K B:307;
Part of Protein;
none;
submit data
39.098 K [K+]
EDO B:302;
A:304;
A:303;
B:303;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
NA A:310;
A:305;
A:306;
B:306;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
22.99 Na [Na+]
EP1 B:305;
A:308;
Invalid;
Invalid;
none;
none;
submit data
252.331 C9 H20 N2 O4 S C1CN(...
CL A:307;
B:304;
A:309;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
35.453 Cl [Cl-]
LI A:311;
Part of Protein;
none;
submit data
6.941 Li [Li+]
FON A:301;
Valid;
none;
submit data
473.439 C20 H23 N7 O7 c1cc(...
TYD B:301;
Valid;
none;
submit data
402.188 C10 H16 N2 O11 P2 CC1=C...
0FX A:302;
Valid;
none;
submit data
547.345 C16 H27 N3 O14 P2 C[C@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5VYQ 1.6 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE N-FORMYLTRANSFERASE RV3404C FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH YDP-QUI4N AND FO MYCOBACTERIUM TUBERCULOSIS CAS/NITR204ORGANISM_TAXID: 1310114 FORMYLTRANSFERASE DEOXYSUGAR TRANSFERASE
Ref.: BIOCHEMICAL INVESTIGATION OF RV3404C FROM MYCOBACTE TUBERCULOSIS. BIOCHEMISTRY V. 56 3818 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 5VYQ - FON C20 H23 N7 O7 c1cc(ccc1C....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 5VYQ - FON C20 H23 N7 O7 c1cc(ccc1C....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 4NV1 - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
2 4YFY - 0FX C16 H27 N3 O14 P2 C[C@@H]1[C....
3 5VYQ - FON C20 H23 N7 O7 c1cc(ccc1C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: FON; Similar ligands found: 20
No: Ligand ECFP6 Tc MDL keys Tc
1 FON 1 1
2 FFO 0.683168 1
3 TLL 0.663551 0.931507
4 C2F 0.550459 0.957747
5 THF 0.536364 0.943662
6 MHF 0.535714 0.881579
7 DHF 0.523364 0.926471
8 1YJ 0.518182 0.926471
9 THG 0.518182 0.926471
10 THH 0.486726 0.8
11 21V 0.469027 0.847222
12 DDF 0.469027 0.847222
13 DZF 0.447368 0.788732
14 FOL 0.447368 0.802817
15 TMF 0.428571 0.866667
16 9L9 0.420561 0.855072
17 LYA 0.415929 0.72973
18 MEF 0.413223 0.881579
19 1YA 0.413223 0.970588
20 83A 0.40678 0.77027
Ligand no: 2; Ligand: TYD; Similar ligands found: 88
No: Ligand ECFP6 Tc MDL keys Tc
1 TYD 1 1
2 TTP 0.884058 1
3 TMP 0.80597 0.985714
4 TLO 0.716049 0.945205
5 DAU 0.694118 0.932432
6 18T 0.682353 0.932432
7 TDX 0.682353 0.945205
8 3R2 0.682353 0.92
9 1JB 0.682353 0.932432
10 TRH 0.682353 0.932432
11 ATY 0.670886 0.945205
12 3YN 0.666667 0.932432
13 DWN 0.666667 0.907895
14 T3F 0.666667 0.907895
15 T3Q 0.666667 0.907895
16 TBD 0.662338 0.958904
17 0N2 0.659091 0.896104
18 T46 0.659091 0.932432
19 AZD 0.654321 0.907895
20 MMF 0.651685 0.907895
21 0FX 0.651685 0.907895
22 LLT 0.641791 0.873239
23 THM 0.641791 0.873239
24 QDM 0.637363 0.896104
25 AKM 0.630435 0.886076
26 FNF 0.630435 0.92
27 JHZ 0.630435 0.884615
28 1YF 0.630435 0.92
29 4TG 0.623656 0.92
30 DUD 0.61039 0.957143
31 0DN 0.6 0.833333
32 UFP 0.6 0.905405
33 DT DT DT DT DT 0.582418 0.945205
34 QUH 0.58 0.907895
35 FUH 0.58 0.907895
36 T5A 0.572816 0.841463
37 5HU 0.571429 0.971831
38 BRU 0.571429 0.905405
39 FDM 0.564103 0.918919
40 NYM 0.564103 0.958333
41 5IU 0.564103 0.905405
42 DT DT PST 0.56383 0.881579
43 T3P 0.56 0.943662
44 THP 0.556962 0.971429
45 ATM 0.542169 0.894737
46 D3T 0.542169 0.971831
47 DUT 0.542169 0.957143
48 TXS 0.538462 0.789474
49 YYY 0.536585 0.891892
50 T3S 0.525 0.789474
51 BVP 0.52381 0.944444
52 ABT 0.521739 0.884615
53 DT DT DT 0.511364 0.878378
54 D4D 0.506024 0.928571
55 7SG 0.504274 0.864198
56 TQP 0.504274 0.864198
57 T5K 0.5 0.853659
58 TPE 0.5 0.894737
59 DT ME6 DT 0.5 0.87013
60 T4K 0.5 0.853659
61 2DT 0.5 0.957747
62 4TA 0.486486 0.807229
63 DCP 0.477273 0.891892
64 8DD 0.473118 0.8125
65 AZZ 0.469136 0.779221
66 UMP 0.469136 0.942857
67 DU 0.469136 0.942857
68 8GD 0.467391 0.829268
69 WMJ 0.452632 0.761905
70 D4T 0.449438 0.928571
71 DUP 0.449438 0.930556
72 6U4 0.447917 0.848101
73 DDN 0.439024 0.942857
74 3DT 0.428571 0.835616
75 UC5 0.425287 0.943662
76 ID2 0.423077 0.8
77 DT MA7 DT 0.420635 0.797619
78 8DG 0.418367 0.829268
79 DUN 0.41573 0.930556
80 DUT MG 0.413043 0.864865
81 5GW 0.410526 0.878378
82 DC 0.406977 0.878378
83 DCM 0.406977 0.878378
84 DT DC 0.405405 0.833333
85 ADS THS THS THS 0.403361 0.767442
86 74W 0.4 0.732558
87 D4M 0.4 0.914286
88 74X 0.4 0.732558
Ligand no: 3; Ligand: 0FX; Similar ligands found: 65
No: Ligand ECFP6 Tc MDL keys Tc
1 0FX 1 1
2 T3F 0.804348 1
3 T3Q 0.804348 1
4 TRH 0.802198 0.973333
5 18T 0.802198 0.973333
6 1JB 0.802198 0.973333
7 4TG 0.737374 0.986667
8 MMF 0.731959 0.973684
9 DAU 0.71875 0.947368
10 QDM 0.717172 0.935897
11 1YF 0.71 0.986667
12 FNF 0.71 0.986667
13 TDX 0.708333 0.96
14 T46 0.704082 0.973333
15 0N2 0.686869 0.986842
16 DWN 0.66 0.973684
17 TTP 0.659341 0.907895
18 FUH 0.657407 0.973684
19 QUH 0.657407 0.973684
20 3R2 0.656566 0.935065
21 TYD 0.651685 0.907895
22 3YN 0.627451 0.947368
23 JHZ 0.613208 0.948718
24 AKM 0.613208 0.949367
25 TLO 0.6 0.909091
26 TMP 0.595506 0.894737
27 T5K 0.584 0.891566
28 T4K 0.584 0.891566
29 7SG 0.563492 0.879518
30 TQP 0.563492 0.879518
31 TBD 0.520408 0.873418
32 T5A 0.512397 0.879518
33 DT DT PST 0.486726 0.873418
34 DT DT DT DT DT 0.486486 0.909091
35 0DN 0.477778 0.779221
36 AZD 0.47619 0.851852
37 THM 0.47191 0.815789
38 LLT 0.47191 0.815789
39 JB2 0.470588 0.747126
40 UFP 0.46875 0.825
41 NYM 0.459184 0.921053
42 ATY 0.457143 0.909091
43 5HU 0.44898 0.883117
44 ATM 0.446602 0.839506
45 DUT 0.446602 0.868421
46 4TA 0.44186 0.845238
47 DT ME6 DT 0.44 0.8625
48 THP 0.44 0.881579
49 TXS 0.438776 0.7625
50 T3P 0.4375 0.857143
51 DUD 0.435644 0.868421
52 TPE 0.434783 0.910256
53 BRU 0.434343 0.825
54 D3T 0.432692 0.883117
55 FDM 0.43 0.8375
56 5IU 0.43 0.825
57 T3S 0.43 0.78481
58 UD4 0.42623 0.92
59 DT DT DT 0.412844 0.87013
60 ABT 0.412281 0.831325
61 DCP 0.411215 0.835443
62 BVP 0.40566 0.858974
63 YYY 0.4 0.835443
64 UDX 0.4 0.893333
65 UAD 0.4 0.893333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5VYQ; Ligand: FON; Similar sites found: 25
This union binding pocket(no: 1) in the query (biounit: 5vyq.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5MUL BDP 0.01267 0.41112 2.7451
2 1ZC3 GNP 0.01381 0.41079 4.57143
3 4CT7 TRP 0.005581 0.45205 4.70588
4 1YQC GLV 0.01656 0.41779 4.70588
5 1FQK ALF 0.01427 0.40602 5.44218
6 3G5S FAD 0.03522 0.40317 5.88235
7 4NZ6 DGL 0.01456 0.40738 6.27451
8 1YJQ NAP 0.02726 0.40479 6.27451
9 3R4S SIA 0.00005994 0.41876 9.01961
10 1NVU GTP 0.009601 0.41848 10.241
11 3KUD GDP 0.01292 0.4043 10.8434
12 3DDC GNP 0.02028 0.40264 10.8434
13 2UZI GTP 0.01953 0.40202 10.8434
14 1RC0 KT5 0.000001621 0.44235 18.1818
15 1GAR U89 0.00008113 0.52773 18.3962
16 3DCJ THH 0.0000001169 0.63293 18.6047
17 5VYR GMP 0.00000004561 0.68615 23.5294
18 5VYR B62 0.00000004561 0.68615 23.5294
19 4LXQ TYD 0.0000000165 0.71873 24.3137
20 4LXQ FON 0.0000000165 0.71873 24.3137
21 2BLN U5P 0.0000001745 0.46842 24.3137
22 2BLN FON 0.0000001925 0.46073 24.3137
23 2CFI ZZZ 0.00002823 0.53095 26.2745
24 5UIJ TYD 0.0000001166 0.68331 28.6275
25 4TTS 6DD 0.00001029 0.55583 30.1961
Pocket No.: 2; Query (leader) PDB : 5VYQ; Ligand: TYD; Similar sites found: 8
This union binding pocket(no: 2) in the query (biounit: 5vyq.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5JE0 AZ8 0.04339 0.40516 4.45344
2 5JE0 SAH 0.04339 0.40516 4.45344
3 5GVL GI8 0.02734 0.42185 5.88235
4 5GVL PLG 0.02734 0.42185 5.88235
5 3QVP FAD 0.03642 0.41755 5.88235
6 1DFO PLG 0.01609 0.41319 7.84314
7 5VYR GMP 0.03156 0.4104 23.5294
8 5VYR B62 0.03156 0.4104 23.5294
Pocket No.: 3; Query (leader) PDB : 5VYQ; Ligand: 0FX; Similar sites found: 6
This union binding pocket(no: 3) in the query (biounit: 5vyq.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1QM5 GLC GLC GLC PO4 SGC GLC 0.02484 0.40447 16.4706
2 5VYR GMP 0.0008184 0.47159 23.5294
3 5VYR B62 0.0008184 0.47159 23.5294
4 4LXQ FON 0.0003362 0.49733 24.3137
5 4LXQ TYD 0.0003362 0.49733 24.3137
6 5UIJ TYD 0.00005391 0.54179 28.6275
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