Receptor
PDB id Resolution Class Description Source Keywords
5TE2 1.8 Å EC: 2.6.1.62 CRYSTAL STRUCTURE OF 7,8-DIAMINOPELARGONIC ACID SYNTHASE (BI MYCOBACTERIUM TUBERCULOSIS, COMPLEXED WITH A MECHANISM-BASEI NHIBITOR MYCOBACTERIUM BOVIS (STRAIN ATCC BAA-9AF2122/97) INHIBITOR COMPLEX TRANSAMINASE PLP TRANSFERASE TRANSFERAINHIBITOR COMPLEX MECHANISM-BASED INHIBITOR TRANSFERASE- TRANSFERASE INHIBITOR COMPLEX
Ref.: RATIONAL OPTIMIZATION OF MECHANISM-BASED INHIBITORS DETERMINATION OF THE MICROSCOPIC RATE CONSTANTS OF INACTIVATION. J. AM. CHEM. SOC. V. 139 7132 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO B:503;
 Invalid;
 none;
 submit data
62.068 C2 H6 O2 C(CO)...
PEG B:502;
 Invalid;
 none;
 submit data
106.12 C4 H10 O3 C(COC...
7B9 B:501;
A:501;
 Valid;
Valid;
 Atoms found LESS than expected: % Diff = 0.111;
Atoms found LESS than expected: % Diff = 0.111;
 submit data
399.336 C16 H22 N3 O7 P Cc1c(...
PGE A:502;
 Invalid;
 none;
 submit data
150.173 C6 H14 O4 C(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 (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: 7B9; Similar ligands found: 52
No: Ligand ECFP6 Tc MDL keys Tc
1 7B9 1 1
2 PL8 0.666667 0.957143
3 7TS 0.564706 0.772152
4 PMH 0.5 0.7
5 DCS 0.488889 0.759494
6 IN5 0.47619 0.782609
7 PLG 0.47619 0.826087
8 PXP 0.467532 0.705882
9 5PA 0.465909 0.842857
10 PLS 0.465909 0.826087
11 RW2 0.463158 0.84507
12 PSZ 0.462366 0.746667
13 0LD 0.462264 0.701149
14 PDD 0.45977 0.785714
15 PP3 0.45977 0.785714
16 P1T 0.45977 0.869565
17 PDA 0.45977 0.785714
18 9YM 0.457447 0.802817
19 PL2 0.456522 0.756757
20 IK2 0.454545 0.791667
21 33P 0.454545 0.771429
22 2BK 0.449438 0.785714
23 TLP 0.449438 0.785714
24 2BO 0.449438 0.785714
25 PXG 0.447917 0.8
26 CBA 0.445652 0.753425
27 ILP 0.445652 0.763889
28 C6P 0.444444 0.826087
29 PPD 0.444444 0.852941
30 PMP 0.443038 0.764706
31 PMG 0.44086 0.808219
32 QLP 0.44086 0.808219
33 PLA 0.43956 0.805556
34 PY5 0.43956 0.805556
35 GT1 0.4375 0.638889
36 PY6 0.43617 0.808219
37 HEY 0.43617 0.884058
38 N5F 0.431579 0.869565
39 ORX 0.431579 0.842857
40 EA5 0.431579 0.84507
41 PGU 0.430108 0.855072
42 7XF 0.430108 0.828571
43 PDG 0.430108 0.855072
44 PE1 0.427083 0.842857
45 LPI 0.425532 0.773333
46 AQ3 0.421569 0.857143
47 76U 0.421053 0.816901
48 DN9 0.42 0.789474
49 PL4 0.418367 0.842857
50 3LM 0.416667 0.783784
51 KAM 0.41 0.816901
52 0PR 0.40404 0.84058
Similar Ligands (3D)
Ligand no: 1; Ligand: 7B9; Similar ligands found: 0
No: Ligand Similarity coefficient
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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