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Receptor
PDB id Resolution Class Description Source Keywords
4CXR 1.7 Å EC: 2.6.1.62 MYCOBATERIUM TUBERCULOSIS TRANSAMINASE BIOA COMPLEXED WITH 1-(1,3-BENZOTHIAZOL-2-YL)METHANAMINE MYCOBACTERIUM TUBERCULOSIS TRANSFERASE TRANSAMINASE TUBERCULOSIS PLP
Ref.: INHIBITION OF MYCOBACTERIUM TUBERCULOSIS TRANSAMINA BY ARYL HYDRAZINES AND HYDRAZIDES. CHEMBIOCHEM V. 15 575 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PLP A:501;
B:501;
Invalid;
Invalid;
none;
none;
submit data
247.142 C8 H10 N O6 P Cc1c(...
SO4 B:503;
A:503;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
EDO A:504;
Invalid;
none;
submit data
62.068 C2 H6 O2 C(CO)...
2BG A:502;
Valid;
none;
submit data
164.228 C8 H8 N2 S c1ccc...
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 (31)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6FYQ - PLP C8 H10 N O6 P Cc1c(c(c(c....
2 4WYC Kd = 15 uM 3VS C10 H9 N3 O c1cc(ccc1C....
3 4CXR - 2BG C8 H8 N2 S c1ccc2c(c1....
4 3TFU - PL8 C16 H22 N3 O7 P Cc1c(c(c(c....
5 4MQR - 2B9 C14 H15 N4 O6 P CC1=C(/C(=....
6 4MQP - 2B1 C15 H15 N4 O5 P S Cc1c(c(c(c....
7 4XJO Kd = 132 nM 41O C20 H17 Cl N2 O2 c1cc(cc(c1....
8 5KGS Kd = 74 nM 6SR C21 H20 N2 O4 c1cc2c(cc1....
9 4W1W ic50 = 0.195 uM 3G8 C18 H17 N O3 S CCN(CC)c1c....
10 4WYG Kd = 6.8 uM 3W1 C11 H12 Cl N3 c1cc(ccc1C....
11 4MQQ - 2B6 C16 H15 N4 O6 P S Cc1c(c(c(c....
12 4XEW ic50 = 0.44 uM 40N C16 H10 F N O3 c1ccc(c(c1....
13 4W1V ic50 = 0.659 uM 3GS C16 H14 F N O5 S COC(=O)c1c....
14 4XJP Kd = 108 nM 41N C20 H20 N2 O4 CC(=O)c1cc....
15 4WYF Kd = 21.7 uM 3VX C11 H9 N O2 CC(=O)Nc1c....
16 4WYA Kd = 6.9 uM 3VQ C10 H8 N2 O S c1ccnc(c1)....
17 4W1X - 3G9 C19 H19 Cl N2 O2 CC(=O)c1cc....
18 5KGT - 6SQ C20 H20 Cl N O2 CC(=O)c1cc....
19 4WYE Kd = 41.8 uM 3VW C12 H15 N O c1ccc(cc1)....
20 4CXQ - KAP C9 H17 N O3 C[C@@H](C(....
21 4WYD Kd = 11.7 uM 3VR C12 H15 N3 CNCc1ccc(c....
22 3LV2 - SFG C15 H23 N7 O5 c1nc(c2c(n....
23 5TE2 - 7B9 C16 H22 N3 O7 P Cc1c(c(c(c....
24 4B9B - PLP C8 H10 N O6 P Cc1c(c(c(c....
25 4B98 - PXG C15 H17 N2 O7 P Cc1c(c(c(c....
26 1MLZ - TZA PLP n/a n/a
27 1MLY - ACZ PLP n/a n/a
28 1S07 - PLP C8 H10 N O6 P Cc1c(c(c(c....
29 3DU4 - KAP C9 H17 N O3 C[C@@H](C(....
30 4BA5 - PXG C15 H17 N2 O7 P Cc1c(c(c(c....
31 3A8U - PLP C8 H10 N O6 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 2BG; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 2BG 1 1
2 ABV 0.487805 0.676471
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: 147
This union binding pocket(no: 1) in the query (biounit: 5kgs.bio1) has 38 residues
No: Leader PDB Ligand Sequence Similarity
1 1ZEI CRS None
2 1K1Y MAL 1.21396
3 1PMO PLR 1.31291
4 5W70 9YM 1.34831
5 4AZJ SEP PLP 1.38889
6 2X1E X1E 1.40056
7 2D09 FLV 1.4742
8 3PD6 PMP 1.49626
9 3PDB PMP 1.49626
10 1VJO PLP 1.52672
11 4NCN GTP 1.53173
12 4QYS PLR 1.58371
13 6CBN OZY 1.59817
14 5T96 79J 1.75439
15 1WD4 AHR 1.96937
16 3BOF HCS 1.96937
17 6B2M COA 1.96937
18 5V7I 8Z1 1.96937
19 1LW4 PLP 2.01729
20 1LW4 TLP 2.01729
21 4K2M O1G 2.0316
22 1H5R G1P 2.04778
23 4RKK GLC GLC GLC GLC GLC GLC 2.10843
24 1M32 PLP 2.18579
25 6DND PLP 2.18978
26 5TXR PLP 2.24033
27 1RQ2 CIT 2.35602
28 1U26 IHS 2.37389
29 5E9G GLV 2.407
30 3K6V CIT 2.407
31 5X30 7XF 2.51256
32 5X30 4LM 2.51256
33 5M3Z PLP 2.51256
34 5M3Z PY6 2.51256
35 5X2Z 3LM 2.51256
36 1B9I PXG 2.57732
37 1DJ9 KAM 2.60417
38 4TMZ GSP 2.6087
39 5A1S FLC 2.67857
40 4LNL PLG 2.7027
41 4LNL 2BK 2.7027
42 4LNL 2BO 2.7027
43 1FC4 AKB PLP 2.74314
44 2R5C C6P 2.7972
45 3B8X G4M 2.82051
46 3NNT DQA 2.89855
47 1E5F PLP 2.9703
48 5ZZO FLC 2.98507
49 6CZY PMP 3.03867
50 6EWR PMP 3.0445
51 3NUB UD0 3.06407
52 3I7S PYR 3.08219
53 3ZRR PXG 3.125
54 4HVK PMP 3.14136
55 5MB4 NAG 3.2419
56 2OGA PGU 3.25815
57 4ZG4 VO4 ADP 3.28228
58 1GCK ASP PLP 3.37662
59 3FRK TQP 3.48525
60 1QW9 KHP 3.50109
61 5W19 9TD 3.50109
62 5VEQ PMP 3.64964
63 2Z6J TUI 3.91566
64 3VP6 HLD 3.93873
65 6CD1 PLG 3.95604
66 6CD1 PLS 3.95604
67 1TL2 NDG 4.23729
68 4FMS BDP 4.28212
69 2Z9V PXM 4.33673
70 3WGC PLG 4.39883
71 3VNM SDD 4.43686
72 2FYF PLP 4.59519
73 3RJY GLC 4.6875
74 4IY7 0JO 4.78589
75 4IY7 KOU 4.78589
76 4IYO 0JO 4.78589
77 2Y7I ARG 4.80349
78 5FAW CHT 4.814
79 1O5O U5P 4.814
80 1EX7 5GP 4.83871
81 1U08 PLP 4.92228
82 2WK9 PLG 5.14139
83 2WK9 PLP 5.14139
84 2HHP FLC 5.25164
85 1TF9 PHI 5.28169
86 4ZAH T5K 5.30303
87 1D8C GLV 5.47046
88 3E81 SLB 5.4878
89 1DFO PLG 5.51559
90 3WXM GTP 5.58511
91 3M89 GSP 5.62061
92 4M2K PLP 5.66502
93 5W71 PLP 5.68182
94 2J5V RGP 5.68928
95 5I0H ADP BEF 5.68928
96 1B09 PC 5.82524
97 6CBO DOW 5.92255
98 3WMX THR 6.14525
99 1GZF ADP 6.63507
100 2XRH NIO 7
101 1M7B GTP 7.06522
102 1WYV PLP AOA 7.22101
103 1ONI BEZ 7.24638
104 3T2W BTN 7.37705
105 4ZJS 4P0 7.3913
106 1GUA GNP 7.40741
107 5BVS EIC 7.57576
108 2HK1 FUD 8.09062
109 1GJW GLC 8.53392
110 2JG1 TA6 9.19037
111 1NBU PH2 9.2437
112 2EW1 GNP 9.45274
113 1GWN GTP 10.2439
114 2OUA AES 10.6383
115 2C3W GLC GLC GLC GLC 10.7843
116 4WXG 2BO 11.9159
117 2C5L GTP 12.7168
118 3PH4 AOS 13.0178
119 5K8B PDG 13.3995
120 2ZFZ ARG 13.9241
121 2VQ5 HBA 14.4279
122 1LFD GNP 14.9425
123 1JAC AMG 15.7895
124 5DDW 5B6 16.1926
125 1TOQ AMG 19.5489
126 2CJH AKG 19.5991
127 4ZSY RW2 24.9453
128 4ZM4 PLP 27.1335
129 4ZM4 P3B 27.1335
130 5YKT PMP 29.7593
131 3FQ8 PMP 33.9578
132 5WYF ILP 34.7921
133 4UOX PLP 35.2298
134 4UOX PUT 35.2298
135 4UOX PLP PUT 35.2298
136 1ZC9 PMP 35.2298
137 4ADC PLP 35.7143
138 4AOA IK2 37.4179
139 3DXW ICC 38.512
140 3BS8 PMP 38.5845
141 2YKX AKG 40.2151
142 1SFF IK2 40.3756
143 5G4J EXT 40.4814
144 2OAT PFM 40.919
145 4E3Q PMP 42.2319
146 5G09 6DF 42.6696
147 4UHO PLP 49.2341
Pocket No.: 2; Query (leader) PDB : 5KGS; Ligand: 6SR; Similar sites found with APoc: 26
This union binding pocket(no: 2) in the query (biounit: 5kgs.bio1) has 44 residues
No: Leader PDB Ligand Sequence Similarity
1 3ROE THM 1.50943
2 5A3Y VAL LYS 1.53173
3 1A0T SUC 1.93705
4 1OH2 SUC 1.93705
5 2R5E QLP 2.7972
6 1V6A TRE 3.01205
7 2JFV FLC 3.09278
8 3HR1 PF9 3.68421
9 3RC3 ANP 3.71991
10 4L50 D8X 3.7594
11 5FD0 NAG 3.93873
12 4BNU 9KQ 4.08922
13 3BEO UDP 4.26667
14 1CL2 PPG 4.3038
15 5HW4 SAM 5.64516
16 2YY8 SAM 5.97015
17 5A0U CHT 6.12691
18 2QS8 MET 6.45933
19 1I58 ADP 8.46561
20 2GQS C2R 9.2827
21 2J8R MSL 9.30233
22 3EW2 BTN 9.62963
23 5LWY OLB 14.3836
24 4P5E N6P 14.4737
25 6CAM BGC 16.1017
26 1TX4 ALF GDP 16.9492
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