Receptor
PDB id Resolution Class Description Source Keywords
4wyd 1.35 Å EC: 2.6.1.62 ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE F MYCOBACTERIUM TUBERCULOSIS COMPLEXED WITH A FRAGMENT FROM DS CREENING MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCH37RV) TRANSAMINASE PLP COMPLEX FRAGMENT TRANSFERASE-TRANSFERASE ICOMPLEX
Ref.: FRAGMENT-BASED EXPLORATION OF BINDING SITE FLEXIBIL MYCOBACTERIUM TUBERCULOSIS BIOA. J.MED.CHEM. V. 58 5208 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:509;
B:505;
A:507;
A:505;
B:504;
A:504;
A:510;
B:507;
A:508;
A:506;
B:506;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
EPE A:503;
B:503;
 Invalid;
Invalid;
 none;
none;
 submit data
238.305 C8 H18 N2 O4 S C1CN(...
3VR B:502;
A:502;
 Valid;
Valid;
 none;
none;
 Kd = 11.7 uM
201.268 C12 H15 N3 CNCc1...
PLP A:501;
B:501;
 Invalid;
Invalid;
 none;
none;
 submit data
247.142 C8 H10 N O6 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: 3VR; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 3VR 1 1
2 9VQ 0.604651 0.763158
Similar Ligands (3D)
Ligand no: 1; Ligand: 3VR; Similar ligands found: 151
No: Ligand Similarity coefficient
1 PV4 0.9542
2 9AG 0.9539
3 W1G 0.9482
4 A7Q 0.9409
5 E9P 0.9406
6 5NR 0.9357
7 R7T 0.9354
8 9JH 0.9278
9 YI6 0.9259
10 EPE 0.9250
11 QTD 0.9234
12 3W1 0.9217
13 HX8 0.9217
14 2O8 0.9207
15 MJ5 0.9202
16 J4K 0.9164
17 HXY 0.9142
18 YIE 0.9135
19 S0F 0.9135
20 CH8 0.9126
21 N9M 0.9108
22 G8V 0.9103
23 N2Y 0.9089
24 FPL 0.9063
25 OJD 0.9054
26 IBP 0.9045
27 HGK 0.9044
28 M28 0.9030
29 3S9 0.9024
30 IO2 0.9019
31 5TT 0.9007
32 4FP 0.9007
33 PTR 0.9005
34 HJD 0.8991
35 69K 0.8934
36 4AF 0.8931
37 6C4 0.8924
38 YIH 0.8920
39 5O5 0.8920
40 ENO 0.8919
41 JA3 0.8910
42 S7V 0.8903
43 Q9P 0.8902
44 JF5 0.8897
45 5PP 0.8895
46 TFQ 0.8892
47 A8K 0.8888
48 9X3 0.8881
49 PHQ ALA 0.8880
50 HLP 0.8875
51 REG 0.8874
52 4CF 0.8866
53 VIB 0.8863
54 PZX 0.8860
55 TBJ 0.8853
56 S6P 0.8849
57 M25 0.8845
58 0QA 0.8839
59 F90 0.8832
60 T03 0.8831
61 BZM 0.8828
62 ZZU 0.8827
63 FCW 0.8827
64 B15 0.8825
65 6C5 0.8822
66 UA5 0.8821
67 1OU 0.8818
68 FT2 0.8815
69 VD9 0.8804
70 GJG 0.8802
71 C6Z 0.8797
72 I2E 0.8795
73 TPM 0.8789
74 1FD 0.8788
75 A5P 0.8788
76 3W3 0.8786
77 YIP 0.8775
78 6PG 0.8775
79 22F 0.8768
80 TLT 0.8765
81 3G3 0.8763
82 S8P 0.8761
83 DCN 0.8761
84 FT3 0.8759
85 2UB 0.8755
86 EG0 0.8754
87 P93 0.8753
88 3W6 0.8751
89 ISA 0.8746
90 F6R 0.8745
91 M5A 0.8741
92 PPT 0.8739
93 GGG 0.8736
94 3IP 0.8733
95 LL2 0.8725
96 6FG 0.8722
97 3CX 0.8720
98 R5P 0.8717
99 5RP 0.8716
100 HMZ 0.8705
101 1BN 0.8703
102 0OO 0.8703
103 G6Q 0.8698
104 5R8 0.8694
105 109 0.8694
106 MP5 0.8691
107 K82 0.8689
108 AHC 0.8689
109 PAN 0.8689
110 11X 0.8689
111 SNV 0.8684
112 FQY 0.8683
113 3QO 0.8677
114 GLY GLY GLY 0.8675
115 D1Y 0.8675
116 RES 0.8675
117 4BX 0.8673
118 6C9 0.8671
119 XI7 0.8657
120 AGP 0.8654
121 Z70 0.8653
122 8V8 0.8649
123 M6H 0.8645
124 7Y3 0.8645
125 HPP 0.8640
126 TLJ 0.8635
127 EYJ 0.8634
128 0A1 0.8630
129 S0B 0.8628
130 4WF 0.8623
131 PA5 0.8621
132 EZ1 0.8617
133 GHQ 0.8616
134 A4Z 0.8602
135 5TO 0.8601
136 MPP 0.8597
137 PTB 0.8593
138 NFZ 0.8589
139 KAP 0.8588
140 JW8 0.8583
141 EF0 0.8571
142 BZQ 0.8570
143 EFR 0.8565
144 5SP 0.8558
145 LXP 0.8558
146 SU7 0.8553
147 6FR 0.8529
148 BPW 0.8526
149 MRU 0.8525
150 EGV 0.8523
151 TZM 0.8523
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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