Receptor
PDB id Resolution Class Description Source Keywords
3TFU 1.94 Å EC: 2.6.1.62 CRYSTAL STRUCTURE OF 7,8-DIAMINOPELARGONIC ACID SYNTHASE (BI MYCOBACTERIUM TUBERCULOSIS, POST-REACTION COMPLEX WITH A 3,D IHYDROPYRID-2-ONE HETEROCYCLE INHIBITOR MYCOBACTERIUM TUBERCULOSIS TRANSFERASE TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: MECHANISM-BASED INACTIVATION BY AROMATIZATION OF TH TRANSAMINASE BIOA INVOLVED IN BIOTIN BIOSYNTHESIS I MYCOBATERIUM TUBERCULOSIS. J.AM.CHEM.SOC. V. 133 18194 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DMS B:502;
 Invalid;
 none;
 submit data
78.133 C2 H6 O S CS(=O...
PL8 A:501;
B:501;
 Valid;
Valid;
 none;
none;
 submit data
399.336 C16 H22 N3 O7 P Cc1c(...
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 (19)
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 4W1W ic50 = 0.195 uM 3G8 C18 H17 N O3 S CCN(CC)c1c....
5 4WYG Kd = 6.8 uM 3W1 C11 H12 Cl N3 c1cc(ccc1C....
6 4MQQ - 2B6 C16 H15 N4 O6 P S Cc1c(c(c(c....
7 4XEW ic50 = 0.44 uM 40N C16 H10 F N O3 c1ccc(c(c1....
8 4W1V ic50 = 0.659 uM 3GS C16 H14 F N O5 S COC(=O)c1c....
9 4XJP Kd = 108 nM 41N C20 H20 N2 O4 CC(=O)c1cc....
10 4WYF Kd = 21.7 uM 3VX C11 H9 N O2 CC(=O)Nc1c....
11 4WYA Kd = 6.9 uM 3VQ C10 H8 N2 O S c1ccnc(c1)....
12 4W1X - 3G9 C19 H19 Cl N2 O2 CC(=O)c1cc....
13 5KGT - 6SQ C20 H20 Cl N O2 CC(=O)c1cc....
14 4WYE Kd = 41.8 uM 3VW C12 H15 N O c1ccc(cc1)....
15 4CXQ - KAP C9 H17 N O3 C[C@@H](C(....
16 4WYD Kd = 11.7 uM 3VR C12 H15 N3 CNCc1ccc(c....
17 3LV2 - SFG C15 H23 N7 O5 c1nc(c2c(n....
18 5TE2 - 7B9 C16 H22 N3 O7 P Cc1c(c(c(c....
19 1MLZ - TZA PLP n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: PL8; Similar ligands found: 53
No: Ligand ECFP6 Tc MDL keys Tc
1 PL8 1 1
2 7B9 0.666667 0.957143
3 7TS 0.597561 0.810127
4 DCS 0.517241 0.797468
5 PMH 0.511905 0.7375
6 IN5 0.487805 0.75
7 PLG 0.487805 0.791667
8 PXP 0.48 0.676056
9 PY6 0.477778 0.776316
10 5PA 0.476744 0.808219
11 PLS 0.476744 0.791667
12 PXG 0.473118 0.767123
13 PSZ 0.472527 0.717949
14 PDA 0.470588 0.753425
15 PP3 0.470588 0.753425
16 P1T 0.470588 0.833333
17 PDD 0.470588 0.753425
18 PL2 0.466667 0.727273
19 33P 0.465116 0.739726
20 IK2 0.465116 0.76
21 2BK 0.45977 0.753425
22 TLP 0.45977 0.753425
23 2BO 0.45977 0.753425
24 RW2 0.457447 0.810811
25 CBA 0.455556 0.794521
26 ILP 0.455556 0.733333
27 PPD 0.454545 0.816901
28 C6P 0.454545 0.791667
29 PMP 0.454545 0.732394
30 9YM 0.451613 0.77027
31 PMG 0.450549 0.776316
32 QLP 0.450549 0.849315
33 PLA 0.449438 0.773333
34 PY5 0.449438 0.773333
35 GT1 0.448718 0.613333
36 HEY 0.445652 0.847222
37 0LD 0.443396 0.735632
38 N5F 0.44086 0.833333
39 ORX 0.44086 0.808219
40 3LM 0.44086 0.753247
41 7XF 0.43956 0.794521
42 PDG 0.43956 0.819444
43 PGU 0.43956 0.819444
44 PE1 0.43617 0.808219
45 LPI 0.434783 0.74359
46 76U 0.430108 0.783784
47 DN9 0.428571 0.828947
48 0PR 0.427083 0.805556
49 PL4 0.427083 0.808219
50 EA5 0.425532 0.810811
51 LCS 0.419355 0.740741
52 KAM 0.418367 0.783784
53 AQ3 0.415842 0.821918
Similar Ligands (3D)
Ligand no: 1; Ligand: PL8; Similar ligands found: 1
No: Ligand Similarity coefficient
1 2B9 0.8629
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5KGS; Ligand: 6SR; Similar sites found with APoc: 9
This union binding pocket(no: 1) in the query (biounit: 5kgs.bio1) has 44 residues
No: Leader PDB Ligand Sequence Similarity
1 4ZSY RW2 24.9453
2 4ZM4 PLP 27.1335
3 4ZM4 PLP 27.1335
4 4UOX PLP 35.2298
5 4UOX PLP 35.2298
6 4UOX PUT 35.2298
7 4ADC PLP 35.7143
8 3A8U PLP 47.216
9 3A8U PLP 47.216
Pocket No.: 2; Query (leader) PDB : 5KGS; Ligand: 6SR; Similar sites found with APoc: 8
This union binding pocket(no: 2) in the query (biounit: 5kgs.bio1) has 38 residues
No: Leader PDB Ligand Sequence Similarity
1 4ZSY RW2 24.9453
2 4ZM4 PLP 27.1335
3 4ZM4 PLP 27.1335
4 4UOX PLP 35.2298
5 4UOX PLP 35.2298
6 4UOX PUT 35.2298
7 3A8U PLP 47.216
8 3A8U PLP 47.216
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