Receptor
PDB id Resolution Class Description Source Keywords
6VSE 1.76 Å EC: 1.5.1.3 MYCOBACTERIUM TUBERCULOSIS DIHYDROFOLATE REDUCTASE IN COMPLE (PHENOXYMETHYL)BENZOIC ACID(FRAGMENT 14) MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCH37RV) FOLATE PATHWAY BIOSYNTHETIC PROTEIN
Ref.: USING A FRAGMENT-BASED APPROACH TO IDENTIFY ALTERNA CHEMICAL SCAFFOLDS TARGETING DIHYDROFOLATE REDUCTAS FROMMYCOBACTERIUM TUBERCULOSIS. ACS INFECT DIS. V. 6 2192 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAP B:202;
A:202;
 Valid;
Valid;
 none;
none;
 submit data
743.405 C21 H28 N7 O17 P3 c1cc(...
CO B:201;
A:201;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
58.933 Co [Co+2...
PO4 B:204;
 Invalid;
 none;
 submit data
94.971 O4 P [O-]P...
4RG B:203;
 Valid;
 none;
 Kd = 0.5 mM
228.243 C14 H12 O3 c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2CIG 1.9 Å EC: 1.5.1.3 DIHYDROFOLATE REDUCTASE FROM MYCOBACTERIUM TUBERCULOSIS INHI THE ACYCLIC 4R ISOMER OF INH-NADP A DERIVATIVE OF THE PRODRI SONIAZID. MYCOBACTERIUM TUBERCULOSIS NADP ISONIAZID REDUCTASE INHIBITOR BISUBSTRATE TUBERCULOXIDOREDUCTASE ONE-CARBON METABOLISM
Ref.: MYCOBACTERIUM TUBERCULOSIS DIHYDROFOLATE REDUCTASE TARGET FOR ISONIAZID NAT.STRUCT.MOL.BIOL. V. 13 408 2006
Members (23)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 30 families.
1 6VSF Kd = 2.7 mM RKY C13 H14 O5 c1cc2c(cc1....
2 6VS6 - RKV C9 H8 N2 O3 Cn1c(cc(n1....
3 6NNE Kd = 2.2 uM KUP C13 H16 N4 O2 COc1ccc(cc....
4 6VV7 Kd = 34 uM RPM C22 H21 N3 O3 Cc1ccc2c(c....
5 6VS9 Kd = 3.2 mM RK4 C13 H17 N O2 c1cc(cc(c1....
6 6NNH - 1CY C11 H14 Cl N5 CC1(N=C(N=....
7 6VVB Kd = 0.095 mM RQ4 C17 H11 F3 N2 O2 S Cc1c(cc(c(....
8 2CIG Ki = 1 nM 1DG C27 H33 N8 O18 P3 c1cnccc1C(....
9 1DG8 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
10 6VSE Kd = 0.5 mM 4RG C14 H12 O3 c1ccc(cc1)....
11 6NND - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
12 6NNI - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
13 1DG5 Ki = 88 uM TOP C14 H18 N4 O3 COc1cc(cc(....
14 6VS5 Kd = 641 uM 9FH C11 H10 N2 O2 Cc1c(cnn1c....
15 6VSG - X0V C7 H7 F3 N2 c1cc(c(cc1....
16 6VS8 - RJY C7 H9 N O2 S CCOC(=O)c1....
17 6NNC - LYA C20 H21 N5 O6 c1cc(ccc1C....
18 6VSD Kd = 0.75 mM JBB C12 H10 O2 S2 c1cc(cc(c1....
19 6VV6 Kd = 192 uM RPJ C21 H18 F N3 O3 c1ccc2c(c1....
20 1DF7 Ki = 11 nM MTX C20 H22 N8 O5 CN(Cc1cnc2....
21 5JA3 ic50 = 173 nM U06 C23 H22 N4 O3 CCc1c(c(nc....
22 1DG7 Ki = 187 nM WRB C14 H20 Br N5 O2 CC1(N=C(N=....
23 6VV9 - RQ1 C22 H21 N3 O3 c1ccc(cc1)....
70% Homology Family (28)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 24 families.
1 6VSF Kd = 2.7 mM RKY C13 H14 O5 c1cc2c(cc1....
2 6VS6 - RKV C9 H8 N2 O3 Cn1c(cc(n1....
3 6NNE Kd = 2.2 uM KUP C13 H16 N4 O2 COc1ccc(cc....
4 6VV7 Kd = 34 uM RPM C22 H21 N3 O3 Cc1ccc2c(c....
5 6VS9 Kd = 3.2 mM RK4 C13 H17 N O2 c1cc(cc(c1....
6 6NNH - 1CY C11 H14 Cl N5 CC1(N=C(N=....
7 6VVB Kd = 0.095 mM RQ4 C17 H11 F3 N2 O2 S Cc1c(cc(c(....
8 2CIG Ki = 1 nM 1DG C27 H33 N8 O18 P3 c1cnccc1C(....
9 1DG8 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
10 6VSE Kd = 0.5 mM 4RG C14 H12 O3 c1ccc(cc1)....
11 6NND - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
12 6NNI - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
13 1DG5 Ki = 88 uM TOP C14 H18 N4 O3 COc1cc(cc(....
14 6VS5 Kd = 641 uM 9FH C11 H10 N2 O2 Cc1c(cnn1c....
15 6VSG - X0V C7 H7 F3 N2 c1cc(c(cc1....
16 6VS8 - RJY C7 H9 N O2 S CCOC(=O)c1....
17 6NNC - LYA C20 H21 N5 O6 c1cc(ccc1C....
18 6VSD Kd = 0.75 mM JBB C12 H10 O2 S2 c1cc(cc(c1....
19 6VV6 Kd = 192 uM RPJ C21 H18 F N3 O3 c1ccc2c(c1....
20 1DF7 Ki = 11 nM MTX C20 H22 N8 O5 CN(Cc1cnc2....
21 5JA3 ic50 = 173 nM U06 C23 H22 N4 O3 CCc1c(c(nc....
22 1DG7 Ki = 187 nM WRB C14 H20 Br N5 O2 CC1(N=C(N=....
23 6VV9 - RQ1 C22 H21 N3 O3 c1ccc(cc1)....
24 4KL9 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
25 4KNE Kd = 1.26 uM 1CY C11 H14 Cl N5 CC1(N=C(N=....
26 4KM2 Kd = 1.43 uM TOP C14 H18 N4 O3 COc1cc(cc(....
27 4KLX - ATR C10 H16 N5 O13 P3 c1nc(c2c(n....
28 4KM0 Kd = 0.91 uM CP6 C12 H13 Cl N4 CCc1c(c(nc....
50% Homology Family (28)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 15 families.
1 6VSF Kd = 2.7 mM RKY C13 H14 O5 c1cc2c(cc1....
2 6VS6 - RKV C9 H8 N2 O3 Cn1c(cc(n1....
3 6NNE Kd = 2.2 uM KUP C13 H16 N4 O2 COc1ccc(cc....
4 6VV7 Kd = 34 uM RPM C22 H21 N3 O3 Cc1ccc2c(c....
5 6VS9 Kd = 3.2 mM RK4 C13 H17 N O2 c1cc(cc(c1....
6 6NNH - 1CY C11 H14 Cl N5 CC1(N=C(N=....
7 6VVB Kd = 0.095 mM RQ4 C17 H11 F3 N2 O2 S Cc1c(cc(c(....
8 2CIG Ki = 1 nM 1DG C27 H33 N8 O18 P3 c1cnccc1C(....
9 1DG8 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
10 6VSE Kd = 0.5 mM 4RG C14 H12 O3 c1ccc(cc1)....
11 6NND - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
12 6NNI - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
13 1DG5 Ki = 88 uM TOP C14 H18 N4 O3 COc1cc(cc(....
14 6VS5 Kd = 641 uM 9FH C11 H10 N2 O2 Cc1c(cnn1c....
15 6VSG - X0V C7 H7 F3 N2 c1cc(c(cc1....
16 6VS8 - RJY C7 H9 N O2 S CCOC(=O)c1....
17 6NNC - LYA C20 H21 N5 O6 c1cc(ccc1C....
18 6VSD Kd = 0.75 mM JBB C12 H10 O2 S2 c1cc(cc(c1....
19 6VV6 Kd = 192 uM RPJ C21 H18 F N3 O3 c1ccc2c(c1....
20 1DF7 Ki = 11 nM MTX C20 H22 N8 O5 CN(Cc1cnc2....
21 5JA3 ic50 = 173 nM U06 C23 H22 N4 O3 CCc1c(c(nc....
22 1DG7 Ki = 187 nM WRB C14 H20 Br N5 O2 CC1(N=C(N=....
23 6VV9 - RQ1 C22 H21 N3 O3 c1ccc(cc1)....
24 4KL9 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
25 4KNE Kd = 1.26 uM 1CY C11 H14 Cl N5 CC1(N=C(N=....
26 4KM2 Kd = 1.43 uM TOP C14 H18 N4 O3 COc1cc(cc(....
27 4KLX - ATR C10 H16 N5 O13 P3 c1nc(c2c(n....
28 4KM0 Kd = 0.91 uM CP6 C12 H13 Cl N4 CCc1c(c(nc....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: NAP; Similar ligands found: 140
No: Ligand ECFP6 Tc MDL keys Tc
1 NAP 1 1
2 NA0 0.881356 0.986301
3 TAP 0.872881 0.934211
4 NDO 0.840336 0.972603
5 NAD 0.811966 0.986111
6 N01 0.733871 0.958904
7 NAD IBO 0.716667 0.972222
8 NAD TDB 0.716667 0.972222
9 A3D 0.712 0.972603
10 NBP 0.707692 0.935065
11 NHD 0.68254 0.958904
12 NJP 0.661417 0.972973
13 NFD 0.658915 0.934211
14 DND 0.619048 0.959459
15 AMP NAD 0.606061 0.958904
16 ZID 0.605839 0.972603
17 NAQ 0.59854 0.922078
18 ATR 0.59292 0.917808
19 NAE 0.591241 0.946667
20 NDE 0.58042 0.986301
21 A22 0.571429 0.958904
22 NAJ 0.567164 0.986111
23 A2R 0.563025 0.932432
24 NDC 0.561644 0.922078
25 NA7 0.552846 0.907895
26 ODP 0.551471 0.935065
27 A2P 0.539823 0.930556
28 8ID 0.537313 0.910256
29 NAD BBN 0.525974 0.865854
30 NPW 0.525547 0.8875
31 NZQ 0.521739 0.910256
32 CNA 0.521739 0.959459
33 NAD CJ3 0.519231 0.835294
34 NDP 0.514493 0.922078
35 PO4 PO4 A A A A PO4 0.503937 0.930556
36 1DG 0.503401 0.922078
37 DG1 0.503401 0.922078
38 TXP 0.5 0.922078
39 NMN AMP PO4 0.492958 0.921053
40 XNP 0.492958 0.875
41 25L 0.492308 0.958904
42 25A 0.492063 0.972222
43 NAD NDT 0.490909 0.747368
44 NMN 0.486726 0.888889
45 NGD 0.485714 0.935065
46 9JJ 0.481707 0.8875
47 2AM 0.477876 0.891892
48 NDP DTT 0.461538 0.843373
49 ADP 0.458333 0.945205
50 ADP MG 0.454545 0.944444
51 ADP BEF 0.454545 0.944444
52 A7R 0.452555 0.846154
53 PAP 0.451613 0.931507
54 A2D 0.445378 0.945205
55 AN2 0.442623 0.932432
56 7L1 0.441558 0.777778
57 ADP PO3 0.44 0.944444
58 AGS 0.44 0.896104
59 ATP MG 0.44 0.944444
60 M33 0.439024 0.906667
61 AR6 AR6 0.438849 0.945205
62 BA3 0.438017 0.945205
63 VO4 ADP 0.4375 0.945946
64 BEF ADP 0.436508 0.918919
65 OAD 0.43609 0.92
66 ADP BMA 0.43609 0.92
67 DQV 0.435714 0.958904
68 HEJ 0.435484 0.945205
69 ATP 0.435484 0.945205
70 OOB 0.435115 0.958904
71 AP5 0.434426 0.945205
72 B4P 0.434426 0.945205
73 GAP 0.433071 0.92
74 0WD 0.432432 0.922078
75 5FA 0.432 0.945205
76 2A5 0.432 0.87013
77 AQP 0.432 0.945205
78 AT4 0.430894 0.907895
79 HQG 0.430769 0.932432
80 00A 0.428571 0.909091
81 8LQ 0.427481 0.907895
82 DAL AMP 0.427481 0.932432
83 CA0 0.427419 0.92
84 ANP MG 0.426357 0.932432
85 ALF ADP 0.426357 0.871795
86 9X8 0.425373 0.871795
87 KG4 0.424 0.92
88 ACP 0.424 0.92
89 NAJ PZO 0.423841 0.897436
90 9SN 0.423358 0.897436
91 WAQ 0.422222 0.884615
92 ACQ 0.421875 0.92
93 V3L 0.421875 0.945205
94 ADQ 0.421053 0.92
95 AR6 0.420635 0.918919
96 APR 0.420635 0.918919
97 ATP A 0.42029 0.958333
98 ATP A A A 0.42029 0.958333
99 CO7 0.419753 0.786517
100 3OD 0.419118 0.92
101 1ZZ 0.419118 0.841463
102 DLL 0.41791 0.958904
103 AD9 0.417323 0.92
104 OVE 0.416667 0.857143
105 NAX 0.416667 0.875
106 QA7 0.416667 0.896104
107 MYR AMP 0.416058 0.841463
108 AV2 0.415385 0.868421
109 A3P 0.414634 0.944444
110 NNR 0.414414 0.72973
111 ALF ADP 3PG 0.413793 0.8625
112 OMR 0.413793 0.831325
113 6YZ 0.412214 0.92
114 ANP 0.410853 0.92
115 A1R 0.410448 0.860759
116 45A 0.409836 0.893333
117 ABM 0.409836 0.893333
118 AMP 0.408333 0.944444
119 A 0.408333 0.944444
120 SON 0.408 0.933333
121 PPS 0.407692 0.829268
122 8LE 0.407692 0.896104
123 5AL 0.407692 0.932432
124 NAI 0.406897 0.909091
125 7D3 0.406504 0.857143
126 AMP MG 0.404959 0.930556
127 ADX 0.404762 0.829268
128 ATF 0.40458 0.907895
129 3UK 0.404412 0.945946
130 AMP DBH 0.404255 0.894737
131 139 0.402685 0.875
132 50T 0.401575 0.906667
133 8LH 0.401515 0.907895
134 SRP 0.401515 0.907895
135 B5V 0.40146 0.933333
136 3AM 0.4 0.90411
137 B5M 0.4 0.921053
138 A3R 0.4 0.860759
139 KMQ 0.4 0.883117
140 FA5 0.4 0.933333
Ligand no: 2; Ligand: 4RG; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 4RG 1 1
2 VJJ 0.428571 0.857143
Similar Ligands (3D)
Ligand no: 1; Ligand: NAP; Similar ligands found: 4
No: Ligand Similarity coefficient
1 TXD 0.9146
2 6V0 0.9079
3 AP0 0.8967
4 TXE 0.8646
Ligand no: 2; Ligand: 4RG; Similar ligands found: 243
No: Ligand Similarity coefficient
1 EMU 0.9606
2 MH5 0.9594
3 JBB 0.9585
4 EEY 0.9584
5 GW9 0.9579
6 KVD 0.9524
7 Z3R 0.9494
8 U14 0.9407
9 Q92 0.9397
10 LI4 0.9373
11 T34 0.9373
12 NU3 0.9302
13 TVC 0.9301
14 245 0.9299
15 H35 0.9295
16 Q2S 0.9288
17 47V 0.9279
18 QS4 0.9266
19 UV4 0.9266
20 LFK 0.9264
21 HCC 0.9260
22 8KW 0.9258
23 8M5 0.9255
24 NZ4 0.9246
25 U12 0.9245
26 HHV 0.9242
27 IK1 0.9237
28 AEY 0.9202
29 7VY 0.9199
30 TVZ 0.9192
31 T21 0.9188
32 GQZ 0.9185
33 7G2 0.9172
34 HWH 0.9168
35 12R 0.9159
36 CMG 0.9154
37 STL 0.9137
38 ESJ 0.9131
39 JF5 0.9128
40 MT6 0.9122
41 A45 0.9122
42 IDZ 0.9111
43 FHV 0.9108
44 108 0.9105
45 F91 0.9105
46 ASE 0.9102
47 0QX 0.9083
48 UN4 0.9082
49 OLU 0.9080
50 KTV 0.9076
51 0OP 0.9071
52 ZEA 0.9066
53 U4J 0.9063
54 NRG 0.9061
55 D59 0.9051
56 NW1 0.9045
57 UAY 0.9043
58 LR2 0.9042
59 6FX 0.9040
60 MR6 0.9040
61 4K2 0.9035
62 5E5 0.9028
63 C4E 0.9026
64 LZ7 0.9024
65 3TI 0.9021
66 5B2 0.9017
67 338 0.9013
68 KTM 0.9012
69 6TJ 0.9011
70 ML1 0.9010
71 NXY 0.9009
72 NFZ 0.9006
73 LJ2 0.9003
74 QEI 0.9002
75 QC1 0.9001
76 8CC 0.8997
77 NIY 0.8994
78 DN8 0.8992
79 NX1 0.8991
80 ZIP 0.8991
81 RDV 0.8990
82 U13 0.8990
83 RK4 0.8989
84 ZRK 0.8988
85 G2V 0.8983
86 H0V 0.8980
87 IW3 0.8979
88 9JT 0.8977
89 WA2 0.8976
90 1HP 0.8967
91 IEE 0.8965
92 JSX 0.8949
93 HH6 0.8943
94 BVB 0.8933
95 E9L 0.8933
96 7EH 0.8930
97 00G 0.8927
98 6H2 0.8926
99 2QU 0.8920
100 MR5 0.8917
101 YIP 0.8917
102 PIT 0.8916
103 4P9 0.8912
104 MR4 0.8912
105 ZRL 0.8909
106 BMC 0.8907
107 6C8 0.8903
108 6F3 0.8899
109 VXP 0.8896
110 GOW 0.8889
111 5TO 0.8887
112 FER 0.8885
113 1XS 0.8880
114 EFT 0.8877
115 JGY 0.8877
116 QUG 0.8876
117 P4T 0.8872
118 F18 0.8870
119 4YE 0.8868
120 2UV 0.8868
121 T61 0.8868
122 XYP XIM 0.8866
123 0UL 0.8865
124 RE2 0.8861
125 3CA 0.8859
126 DFV 0.8857
127 4L2 0.8856
128 0SY 0.8854
129 3NM 0.8852
130 4YF 0.8850
131 6XC 0.8846
132 RNP 0.8845
133 SU9 0.8844
134 DDC 0.8842
135 O2Q 0.8841
136 H32 0.8839
137 PIQ 0.8835
138 ZEZ 0.8831
139 Q7U 0.8819
140 0XR 0.8818
141 0OM 0.8817
142 BXS 0.8814
143 JCQ 0.8808
144 JVB 0.8807
145 3WK 0.8805
146 2QV 0.8804
147 34L 0.8802
148 GF7 0.8801
149 0FS 0.8800
150 5R9 0.8800
151 IW5 0.8800
152 3WL 0.8797
153 3EB 0.8794
154 5WW 0.8785
155 LI7 0.8779
156 83D 0.8778
157 SNJ 0.8778
158 LVP 0.8774
159 15I 0.8773
160 F5N 0.8769
161 EDG AHR 0.8767
162 A9B 0.8765
163 VT3 0.8759
164 XEV 0.8756
165 28A 0.8754
166 OUA 0.8754
167 28B 0.8753
168 IMK 0.8744
169 41L 0.8739
170 AHR AHR 0.8737
171 6NZ 0.8735
172 IW4 0.8735
173 EDZ 0.8732
174 CDJ 0.8730
175 OUG 0.8729
176 AV7 0.8727
177 A51 0.8726
178 A0R 0.8726
179 3JC 0.8719
180 0DF 0.8713
181 SIJ 0.8706
182 VXM 0.8701
183 IPJ 0.8699
184 272 0.8697
185 72G 0.8696
186 7FZ 0.8693
187 STV 0.8692
188 LJ1 0.8692
189 FZB 0.8687
190 5HG 0.8685
191 S7V 0.8683
192 XYS XYS 0.8681
193 T5J 0.8681
194 6T5 0.8678
195 MHB 0.8677
196 M01 0.8677
197 IQQ 0.8674
198 4GU 0.8669
199 C0V 0.8666
200 QDR 0.8664
201 V2Z 0.8663
202 4G2 0.8663
203 FDZ 0.8662
204 K4T 0.8662
205 DXK 0.8657
206 L5D 0.8655
207 LLG 0.8641
208 BBP 0.8639
209 HAN 0.8638
210 QUE 0.8635
211 CBE 0.8633
212 DMB 0.8632
213 5NN 0.8630
214 EBB 0.8630
215 3D8 0.8630
216 W8L 0.8630
217 5KN 0.8629
218 F13 0.8618
219 Q4G 0.8615
220 0X2 0.8612
221 B5A 0.8612
222 9M9 0.8602
223 A9E 0.8599
224 N9M 0.8598
225 AOY 0.8597
226 833 0.8597
227 CFK 0.8594
228 YE7 0.8588
229 S0B 0.8573
230 KWV 0.8573
231 PE2 0.8569
232 2D2 0.8564
233 SQM 0.8564
234 2PW 0.8560
235 43O 0.8559
236 L2K 0.8555
237 1OT 0.8548
238 AVX 0.8537
239 BJ4 0.8531
240 20P 0.8527
241 SNP 0.8527
242 M08 0.8525
243 FX5 0.8514
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2CIG; Ligand: 1DG; Similar sites found with APoc: 5
This union binding pocket(no: 1) in the query (biounit: 2cig.bio1) has 68 residues
No: Leader PDB Ligand Sequence Similarity
1 3NRR D16 21.3836
2 3NRR NAP 21.3836
3 3NRR NAP 21.3836
4 3NRR D16 21.3836
5 5DXV NAP 37.1795
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