Receptor
PDB id Resolution Class Description Source Keywords
4W1V 2.24 Å EC: 2.6.1.62 CRYSTAL STRUCTURE OF 7,8-DIAMINOPELARGONIC ACID SYNTHASE (BI MYCOBACTERIUM TUBERCULOSIS, COMPLEXED WITH A THIAZOLE INHIB MYCOBACTERIUM TUBERCULOSIS INHIBITOR COMPLEX TRANSAMINASE PLP TRANSFERASE-TRANSFERASE COMPLEX
Ref.: TARGET-BASED IDENTIFICATION OF WHOLE-CELL ACTIVE IN OF BIOTIN BIOSYNTHESIS IN MYCOBACTERIUM TUBERCULOSI CHEM.BIOL. V. 22 76 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PEG A:503;
Invalid;
none;
submit data
106.12 C4 H10 O3 C(COC...
PLP A:501;
B:501;
Invalid;
Invalid;
none;
none;
submit data
247.142 C8 H10 N O6 P Cc1c(...
EDO B:507;
B:505;
B:503;
B:506;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
CL B:504;
Invalid;
none;
submit data
35.453 Cl [Cl-]
3GS B:502;
A:502;
Valid;
Valid;
none;
none;
ic50 = 0.659 uM
351.349 C16 H14 F N O5 S COC(=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5KGS 2.1 Å EC: 2.6.1.62 CRYSTAL STRUCTURE OF 7,8-DIAMINOPELARGONIC ACID SYNTHASE (BI MYCOBACTERIUM TUBERCULOSIS, COMPLEXED WITH AN INHIBITOR OPTF ROM HTS LEAD: 5-[4-(1,3-BENZODIOXOL-5-YLCARBONYL)PIPERAZIN3- DIHYDROINDEN-1-ONE MYCOBACTERIUM BOVIS (STRAIN ATCC BAA-9AF2122/97) TRANSAMINASE PLP TRANSFERASE TRANSFERASE-INHIBITOR COMPLETRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: STRUCTURE-BASED OPTIMIZATION OF PYRIDOXAL 5'-PHOSPHATE-DEPENDENT TRANSAMINASE ENZYME (BIOA) I THAT TARGET BIOTIN BIOSYNTHESIS IN MYCOBACTERIUM TUBERCULOSIS. J. MED. CHEM. V. 60 5507 2017
Members (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4WYC Kd = 15 uM 3VS C10 H9 N3 O c1cc(ccc1C....
2 4CXR - 2BG C8 H8 N2 S c1ccc2c(c1....
3 3TFU - PL8 C16 H22 N3 O7 P Cc1c(c(c(c....
4 4MQR - 2B9 C14 H15 N4 O6 P CC1=C(/C(=....
5 4MQP - 2B1 C15 H15 N4 O5 P S Cc1c(c(c(c....
6 4XJO Kd = 132 nM 41O C20 H17 Cl N2 O2 c1cc(cc(c1....
7 5KGS Kd = 74 nM 6SR C21 H20 N2 O4 c1cc2c(cc1....
8 4W1W ic50 = 0.195 uM 3G8 C18 H17 N O3 S CCN(CC)c1c....
9 4WYG Kd = 6.8 uM 3W1 C11 H12 Cl N3 c1cc(ccc1C....
10 4MQQ - 2B6 C16 H15 N4 O6 P S Cc1c(c(c(c....
11 4XEW ic50 = 0.44 uM 40N C16 H10 F N O3 c1ccc(c(c1....
12 4W1V ic50 = 0.659 uM 3GS C16 H14 F N O5 S COC(=O)c1c....
13 4XJP Kd = 108 nM 41N C20 H20 N2 O4 CC(=O)c1cc....
14 4WYF Kd = 21.7 uM 3VX C11 H9 N O2 CC(=O)Nc1c....
15 4WYA Kd = 6.9 uM 3VQ C10 H8 N2 O S c1ccnc(c1)....
16 4W1X - 3G9 C19 H19 Cl N2 O2 CC(=O)c1cc....
17 5KGT - 6SQ C20 H20 Cl N O2 CC(=O)c1cc....
18 4WYE Kd = 41.8 uM 3VW C12 H15 N O c1ccc(cc1)....
19 4CXQ - KAP C9 H17 N O3 C[C@@H](C(....
20 4WYD Kd = 11.7 uM 3VR C12 H15 N3 CNCc1ccc(c....
21 3LV2 - SFG C15 H23 N7 O5 c1nc(c2c(n....
22 5TE2 - 7B9 C16 H22 N3 O7 P Cc1c(c(c(c....
70% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4WYC Kd = 15 uM 3VS C10 H9 N3 O c1cc(ccc1C....
2 4CXR - 2BG C8 H8 N2 S c1ccc2c(c1....
3 3TFU - PL8 C16 H22 N3 O7 P Cc1c(c(c(c....
4 4MQR - 2B9 C14 H15 N4 O6 P CC1=C(/C(=....
5 4MQP - 2B1 C15 H15 N4 O5 P S Cc1c(c(c(c....
6 4XJO Kd = 132 nM 41O C20 H17 Cl N2 O2 c1cc(cc(c1....
7 5KGS Kd = 74 nM 6SR C21 H20 N2 O4 c1cc2c(cc1....
8 4W1W ic50 = 0.195 uM 3G8 C18 H17 N O3 S CCN(CC)c1c....
9 4WYG Kd = 6.8 uM 3W1 C11 H12 Cl N3 c1cc(ccc1C....
10 4MQQ - 2B6 C16 H15 N4 O6 P S Cc1c(c(c(c....
11 4XEW ic50 = 0.44 uM 40N C16 H10 F N O3 c1ccc(c(c1....
12 4W1V ic50 = 0.659 uM 3GS C16 H14 F N O5 S COC(=O)c1c....
13 4XJP Kd = 108 nM 41N C20 H20 N2 O4 CC(=O)c1cc....
14 4WYF Kd = 21.7 uM 3VX C11 H9 N O2 CC(=O)Nc1c....
15 4WYA Kd = 6.9 uM 3VQ C10 H8 N2 O S c1ccnc(c1)....
16 4W1X - 3G9 C19 H19 Cl N2 O2 CC(=O)c1cc....
17 5KGT - 6SQ C20 H20 Cl N O2 CC(=O)c1cc....
18 4WYE Kd = 41.8 uM 3VW C12 H15 N O c1ccc(cc1)....
19 4CXQ - KAP C9 H17 N O3 C[C@@H](C(....
20 4WYD Kd = 11.7 uM 3VR C12 H15 N3 CNCc1ccc(c....
21 3LV2 - SFG C15 H23 N7 O5 c1nc(c2c(n....
22 5TE2 - 7B9 C16 H22 N3 O7 P Cc1c(c(c(c....
50% Homology Family (29)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4WYC Kd = 15 uM 3VS C10 H9 N3 O c1cc(ccc1C....
2 4CXR - 2BG C8 H8 N2 S c1ccc2c(c1....
3 3TFU - PL8 C16 H22 N3 O7 P Cc1c(c(c(c....
4 4MQR - 2B9 C14 H15 N4 O6 P CC1=C(/C(=....
5 4MQP - 2B1 C15 H15 N4 O5 P S Cc1c(c(c(c....
6 4XJO Kd = 132 nM 41O C20 H17 Cl N2 O2 c1cc(cc(c1....
7 5KGS Kd = 74 nM 6SR C21 H20 N2 O4 c1cc2c(cc1....
8 4W1W ic50 = 0.195 uM 3G8 C18 H17 N O3 S CCN(CC)c1c....
9 4WYG Kd = 6.8 uM 3W1 C11 H12 Cl N3 c1cc(ccc1C....
10 4MQQ - 2B6 C16 H15 N4 O6 P S Cc1c(c(c(c....
11 4XEW ic50 = 0.44 uM 40N C16 H10 F N O3 c1ccc(c(c1....
12 4W1V ic50 = 0.659 uM 3GS C16 H14 F N O5 S COC(=O)c1c....
13 4XJP Kd = 108 nM 41N C20 H20 N2 O4 CC(=O)c1cc....
14 4WYF Kd = 21.7 uM 3VX C11 H9 N O2 CC(=O)Nc1c....
15 4WYA Kd = 6.9 uM 3VQ C10 H8 N2 O S c1ccnc(c1)....
16 4W1X - 3G9 C19 H19 Cl N2 O2 CC(=O)c1cc....
17 5KGT - 6SQ C20 H20 Cl N O2 CC(=O)c1cc....
18 4WYE Kd = 41.8 uM 3VW C12 H15 N O c1ccc(cc1)....
19 4CXQ - KAP C9 H17 N O3 C[C@@H](C(....
20 4WYD Kd = 11.7 uM 3VR C12 H15 N3 CNCc1ccc(c....
21 3LV2 - SFG C15 H23 N7 O5 c1nc(c2c(n....
22 5TE2 - 7B9 C16 H22 N3 O7 P Cc1c(c(c(c....
23 4B9B - PLP C8 H10 N O6 P Cc1c(c(c(c....
24 4B98 - PXG C15 H17 N2 O7 P Cc1c(c(c(c....
25 1MLZ - TZA PLP n/a n/a
26 1MLY - ACZ PLP n/a n/a
27 1S07 - PLP C8 H10 N O6 P Cc1c(c(c(c....
28 3DU4 - KAP C9 H17 N O3 C[C@@H](C(....
29 3A8U - PLP C8 H10 N O6 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 3GS; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 3GS 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5KGS; Ligand: 6SR; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5kgs.bio1) has 38 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5KGS; Ligand: 6SR; Similar sites found: 67
This union binding pocket(no: 2) in the query (biounit: 5kgs.bio1) has 44 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1K1Y MAL 0.04667 0.41646 1.21396
2 5W70 9YM 0.001736 0.45459 1.34831
3 4AZJ SEP PLP 0.01166 0.41327 1.38889
4 2X1E X1E 0.01344 0.44539 1.40056
5 3PD6 PMP 0.006602 0.45036 1.49626
6 3PDB PMP 0.009851 0.4371 1.49626
7 1Q8A HCS 0.03345 0.4222 1.96937
8 3BOF HCS 0.03953 0.41792 1.96937
9 4K2M O1G 0.0009075 0.46 2.0316
10 4RKK GLC GLC GLC GLC GLC GLC 0.03297 0.40666 2.10843
11 5HSS 650 0.02441 0.42426 2.15633
12 1M32 PLP 0.01154 0.44668 2.18579
13 5X30 7XF 0.001783 0.45788 2.51256
14 5X30 4LM 0.002683 0.45334 2.51256
15 1DJ9 KAM 0.001853 0.46529 2.60417
16 4TMZ GSP 0.01948 0.40043 2.6087
17 1FC4 AKB PLP 0.007337 0.42884 2.74314
18 2R5E QLP 0.01608 0.40972 2.7972
19 3B8X G4M 0.002517 0.41032 2.82051
20 3NUB UD0 0.005569 0.40394 3.06407
21 1GCK ASP PLP 0.01563 0.4103 3.37662
22 3FRK TQP 0.004708 0.40679 3.48525
23 3E2Y PMP 0.01796 0.42364 3.65854
24 3HR1 PF9 0.0164 0.4065 3.68421
25 3WGC PLG 0.001383 0.47153 4.39883
26 2FYF PLP 0.01281 0.43943 4.59519
27 4IY7 KOU 0.00902 0.42141 4.78589
28 4IY7 0JO 0.009233 0.42094 4.78589
29 4IYO 0JO 0.01114 0.41715 4.78589
30 5FAW CHT 0.01508 0.44003 4.814
31 1U08 PLP 0.008623 0.44425 4.92228
32 1KK8 BEF ADP 0.01616 0.41567 5.19481
33 4ZAH T5K 0.001975 0.42954 5.30303
34 2YY8 MTA 0.001691 0.47642 5.97015
35 2YY8 SAM 0.005811 0.43028 5.97015
36 1GZF ADP 0.02905 0.40329 6.63507
37 1M7B GTP 0.02403 0.40156 7.06522
38 1WYV PLP AOA 0.01047 0.42826 7.22101
39 5BVS EIC 0.02181 0.41248 7.57576
40 2HK1 FUD 0.03906 0.41312 8.09062
41 1I58 ADP 0.02713 0.41097 8.46561
42 3EW2 BTN 0.04333 0.40709 9.62963
43 1ZN7 PRP 0.02954 0.40008 10
44 4WXG 2BO 0.00487 0.42441 11.9159
45 2C5L GTP 0.008941 0.40754 12.7168
46 5O2T GSP 0.01182 0.40238 13.0178
47 1LFD GNP 0.01455 0.40098 14.9425
48 5DDW 5B6 0.00000001377 0.68258 16.1926
49 4ZSY RW2 0.00000000584 0.6995 24.9453
50 4ZM4 PLP 0.0000000465 0.70046 27.1335
51 4ZM4 P3B 0.0000002468 0.63263 27.1335
52 3FQ8 PMP 0.00000005824 0.46161 33.9578
53 5WYF ILP 0.00000003379 0.67259 34.7921
54 4UOX PLP 0.000000002406 0.77615 35.2298
55 4UOX PUT 0.00000001071 0.72253 35.2298
56 4UOX PLP PUT 0.00000003777 0.6868 35.2298
57 1ZC9 PMP 0.0000002619 0.63871 35.2298
58 4ADC PLP 0.000000004251 0.68984 35.7143
59 4AOA IK2 0.000000006928 0.73182 37.4179
60 2YKX AKG 0.001305 0.49202 40.2151
61 1SFF IK2 0.000000001766 0.7319 40.3756
62 5G4J EXT 0.0000001379 0.65186 40.4814
63 2OAT PFM 0.00000001112 0.71235 40.919
64 4E3Q PMP 0.000000001599 0.79731 42.2319
65 5G09 6DF 0.0000000005931 0.75383 42.6696
66 4BA5 PXG 0.0000002468 0.65562 42.6696
67 4UHO PLP 0.0000003882 0.69268 49.2341
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