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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 1443 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 1205 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 187 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 THG 0.518182 0.926471
9 1YJ 0.518182 0.926471
10 THH 0.486726 0.8
11 21V 0.469027 0.847222
12 DDF 0.469027 0.847222
13 FOL 0.447368 0.802817
14 DZF 0.447368 0.788732
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: 87
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 1JB 0.682353 0.932432
7 TRH 0.682353 0.932432
8 3R2 0.682353 0.92
9 18T 0.682353 0.932432
10 TDX 0.682353 0.945205
11 ATY 0.670886 0.945205
12 3YN 0.666667 0.932432
13 DWN 0.666667 0.907895
14 T3Q 0.666667 0.907895
15 T3F 0.666667 0.907895
16 TBD 0.662338 0.958904
17 T46 0.659091 0.932432
18 0N2 0.659091 0.896104
19 AZD 0.654321 0.907895
20 MMF 0.651685 0.907895
21 0FX 0.651685 0.907895
22 THM 0.641791 0.873239
23 LLT 0.641791 0.873239
24 QDM 0.637363 0.896104
25 JHZ 0.630435 0.884615
26 1YF 0.630435 0.92
27 AKM 0.630435 0.886076
28 FNF 0.630435 0.92
29 4TG 0.623656 0.92
30 DT DT DT 0.616279 0.917808
31 DUD 0.61039 0.957143
32 UFP 0.6 0.905405
33 0DN 0.6 0.833333
34 DT DT DT DT DT 0.582418 0.945205
35 QUH 0.58 0.907895
36 FUH 0.58 0.907895
37 T5A 0.572816 0.841463
38 BRU 0.571429 0.905405
39 5HU 0.571429 0.971831
40 DT DT PST 0.569892 0.87013
41 FDM 0.564103 0.918919
42 5IU 0.564103 0.905405
43 NYM 0.564103 0.958333
44 T3P 0.56 0.943662
45 THP 0.556962 0.971429
46 D3T 0.542169 0.971831
47 DUT 0.542169 0.957143
48 ATM 0.542169 0.894737
49 TXS 0.538462 0.789474
50 YYY 0.536585 0.891892
51 T3S 0.525 0.789474
52 BVP 0.52381 0.944444
53 ABT 0.521739 0.884615
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 2DT 0.5 0.957747
59 TPE 0.5 0.894737
60 T4K 0.5 0.853659
61 DT ME6 DT 0.5 0.87013
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 DU 0.469136 0.942857
67 UMP 0.469136 0.942857
68 8GD 0.467391 0.829268
69 WMJ 0.452632 0.761905
70 DUP 0.449438 0.930556
71 D4T 0.449438 0.928571
72 6U4 0.447917 0.848101
73 ADS THS THS THS 0.444444 0.758621
74 DDN 0.439024 0.942857
75 3DT 0.428571 0.835616
76 UC5 0.425287 0.943662
77 ID2 0.423077 0.8
78 DT MA7 DT 0.420635 0.797619
79 8DG 0.418367 0.829268
80 DUN 0.41573 0.930556
81 5GW 0.410526 0.878378
82 DCM 0.406977 0.878378
83 DC 0.406977 0.878378
84 DT DC 0.405405 0.833333
85 74W 0.4 0.732558
86 74X 0.4 0.732558
87 D4M 0.4 0.914286
Ligand no: 3; Ligand: 0FX; Similar ligands found: 66
No: Ligand ECFP6 Tc MDL keys Tc
1 0FX 1 1
2 T3Q 0.804348 1
3 T3F 0.804348 1
4 18T 0.802198 0.973333
5 TRH 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 QUH 0.657407 0.973684
19 FUH 0.657407 0.973684
20 3R2 0.656566 0.935065
21 TYD 0.651685 0.907895
22 3YN 0.627451 0.947368
23 AKM 0.613208 0.949367
24 JHZ 0.613208 0.948718
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 DT 0.509434 0.907895
34 DT DT PST 0.491071 0.8625
35 DT DT DT DT DT 0.486486 0.909091
36 0DN 0.477778 0.779221
37 AZD 0.47619 0.851852
38 LLT 0.47191 0.815789
39 THM 0.47191 0.815789
40 JB2 0.470588 0.747126
41 UFP 0.46875 0.825
42 NYM 0.459184 0.921053
43 ATY 0.457143 0.909091
44 5HU 0.44898 0.883117
45 ATM 0.446602 0.839506
46 DUT 0.446602 0.868421
47 4TA 0.44186 0.845238
48 DT ME6 DT 0.44 0.8625
49 THP 0.44 0.881579
50 TXS 0.438776 0.7625
51 T3P 0.4375 0.857143
52 DUD 0.435644 0.868421
53 TPE 0.434783 0.910256
54 BRU 0.434343 0.825
55 D3T 0.432692 0.883117
56 FDM 0.43 0.8375
57 T3S 0.43 0.78481
58 5IU 0.43 0.825
59 F5P 0.42623 0.92
60 UD4 0.42623 0.92
61 ABT 0.412281 0.831325
62 DCP 0.411215 0.835443
63 BVP 0.40566 0.858974
64 YYY 0.4 0.835443
65 UAD 0.4 0.893333
66 UDX 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 with APoc: 65
This union binding pocket(no: 1) in the query (biounit: 5vyq.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 3KLL MAL 2.35294
2 1D8C SOR 2.35294
3 5MUL BDP 2.7451
4 3FC2 IBI 2.7451
5 4AGS GSH 3.13725
6 3KCC CMP 3.13725
7 5H4S RAM 3.13725
8 2BSA NAP 3.52941
9 2BSA FAD 3.52941
10 2GZ3 NAP 3.92157
11 1ZC3 GNP 4.57143
12 4CT7 TRP 4.70588
13 1YQC GLV 4.70588
14 1LNX URI 4.93827
15 1FQJ ALF 5.44218
16 1FQK ALF 5.44218
17 2C5L GTP 5.78035
18 3G5S FAD 5.88235
19 4NZ6 DGL 6.27451
20 1YJQ NAP 6.27451
21 6FA4 GNP 7.05882
22 6D5G GNP 7.05882
23 6D5E GNP 7.05882
24 6D55 GNP 7.05882
25 4K81 GTP 7.05882
26 6D5M GNP 7.05882
27 6D5H GNP 7.05882
28 6D5L GNP 7.05882
29 6D5V GNP 7.05882
30 6D5J GNP 7.05882
31 6BVJ GNP 7.05882
32 6D56 GNP 7.05882
33 6BVK GNP 7.05882
34 6BVL GNP 7.05882
35 6BVI GNP 7.05882
36 5O2T GSP 7.05882
37 6D59 GNP 7.05882
38 6BVM GNP 7.05882
39 5OCG GNP 7.05882
40 1XF1 CIT 7.84314
41 5X9D 80F 7.84314
42 3R4S SIA 9.01961
43 1HFS L04 9.375
44 1GUA GNP 9.58084
45 1NVV GNP 10.8434
46 3KUD GDP 10.8434
47 3DDC GNP 10.8434
48 2UZI GTP 10.8434
49 1ONI BEZ 13.0435
50 1SBR VIB 17
51 1RC0 KT5 18.1818
52 1GAR U89 18.3962
53 3DCJ THH 18.6047
54 5VYR B62 23.5294
55 5VYR GMP 23.5294
56 2BLN U5P 24.3137
57 2BLN FON 24.3137
58 4LXQ FON 24.3137
59 4LXQ TYD 24.3137
60 2CFI ZZZ 26.2745
61 5UIJ TYD 28.6275
62 4TTS 6DD 30.1961
63 6EDK 1YA 40.553
64 4XCZ FON 47.0588
65 4XCZ T3Q 47.0588
Pocket No.: 2; Query (leader) PDB : 5VYQ; Ligand: TYD; Similar sites found with APoc: 15
This union binding pocket(no: 2) in the query (biounit: 5vyq.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 1HG4 LPP 2.86738
2 5JE0 AZ8 4.45344
3 5JE0 SAH 4.45344
4 5GVL GI8 5.88235
5 5GVL PLG 5.88235
6 3QVP FAD 5.88235
7 2CJF RP4 7.00637
8 1DFO PLG 7.84314
9 5NW7 9C2 7.84314
10 3BWN PMP PHE 8.23529
11 3DVA TPW 8.62745
12 4WXG 2BO 10.1961
13 6CD1 PLS 14.902
14 5VYR B62 23.5294
15 5VYR GMP 23.5294
Pocket No.: 3; Query (leader) PDB : 5VYQ; Ligand: 0FX; Similar sites found with APoc: 16
This union binding pocket(no: 3) in the query (biounit: 5vyq.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 3VPD CIT 6.27451
2 3GDN MXN 7.45098
3 1M26 GAL A2G 8.27068
4 1USF NAP 8.98876
5 3COW 52H 15.6863
6 1QM5 GLC GLC GLC PO4 SGC GLC 16.4706
7 5VYR B62 23.5294
8 5VYR GMP 23.5294
9 4LXQ TYD 24.3137
10 4LXQ FON 24.3137
11 2BLN FON 24.3137
12 2BLN U5P 24.3137
13 5UIJ TYD 28.6275
14 6EDK 1YA 40.553
15 4XCZ FON 47.0588
16 4XCZ T3Q 47.0588
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