Receptor
PDB id Resolution Class Description Source Keywords
6VSF 2.01 Å EC: 1.5.1.3 MYCOBACTERIUM TUBERCULOSIS DIHYDROFOLATE REDUCTASE IN COMPLE (3,4-DIHYDRO-2H-BENZO[B][1,4]DIOXEPIN-7-YL)-4-OXOBUTANOIC A CID(FRAGMENT 16) 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
RKY B:202;
B:201;
A:201;
 Valid;
Valid;
Valid;
 none;
none;
none;
 Kd = 2.7 mM
250.247 C13 H14 O5 c1cc2...
CO A:202;
B:203;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
58.933 Co [Co+2...
PO4 B:207;
B:206;
A:205;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
94.971 O4 P [O-]P...
GOL A:204;
B:205;
 Invalid;
Invalid;
 none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
NAP A:203;
B:204;
 Valid;
Valid;
 none;
none;
 submit data
743.405 C21 H28 N7 O17 P3 c1cc(...
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: RKY; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 RKY 1 1
Ligand no: 2; 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
Similar Ligands (3D)
Ligand no: 1; Ligand: RKY; Similar ligands found: 253
No: Ligand Similarity coefficient
1 2JP 0.9498
2 C0V 0.9473
3 BXS 0.9422
4 KU1 0.9397
5 PW8 0.9368
6 UN9 0.9294
7 F91 0.9293
8 4HG 0.9285
9 WG8 0.9213
10 68C 0.9194
11 00G 0.9185
12 HPK 0.9185
13 0LA 0.9168
14 35K 0.9161
15 0RB 0.9159
16 WLH 0.9148
17 0RY 0.9148
18 JVD 0.9069
19 88S 0.9057
20 20D 0.9056
21 K3T 0.9055
22 Q92 0.9044
23 DFL 0.9044
24 0HY 0.9034
25 SJK 0.9030
26 Q5M 0.9029
27 1R5 0.9028
28 OAQ 0.9022
29 QUB 0.9015
30 5ER 0.9015
31 14X 0.9015
32 TVC 0.9013
33 DE7 0.9005
34 DFV 0.8995
35 HWH 0.8993
36 G30 0.8989
37 1HP 0.8977
38 ESJ 0.8974
39 1CE 0.8973
40 5SJ 0.8964
41 J1K 0.8963
42 39R 0.8961
43 JP3 0.8956
44 ZW2 0.8947
45 14Z 0.8947
46 NKI 0.8944
47 BGK 0.8934
48 MN QAY 0.8932
49 6DQ 0.8924
50 PIQ 0.8922
51 5TT 0.8921
52 NAR 0.8919
53 TYP 0.8917
54 RDV 0.8916
55 ZEA 0.8913
56 0MB 0.8911
57 1V4 0.8909
58 2JX 0.8908
59 K4T 0.8906
60 IXG 0.8900
61 5MX 0.8900
62 YZ9 0.8899
63 4ZF 0.8898
64 5M2 0.8894
65 FNT 0.8891
66 ALJ 0.8888
67 NPS 0.8885
68 ENY 0.8883
69 K8Y 0.8882
70 R4E 0.8881
71 PJK 0.8879
72 108 0.8878
73 MQS 0.8877
74 NEU 0.8876
75 PMM 0.8876
76 QTK 0.8871
77 CX4 0.8869
78 5R9 0.8868
79 SYD 0.8866
80 A63 0.8864
81 EYY 0.8863
82 LIT 0.8860
83 5ZM 0.8859
84 6BK 0.8859
85 C09 0.8857
86 856 0.8850
87 C4E 0.8849
88 EMU 0.8845
89 100 0.8843
90 OQR 0.8842
91 KWK 0.8841
92 JFS 0.8841
93 D1G 0.8839
94 NAL 0.8838
95 WDW 0.8836
96 7KE 0.8836
97 NPX 0.8833
98 LI7 0.8832
99 Q2S 0.8829
100 6DH 0.8828
101 WA2 0.8825
102 4KN 0.8824
103 4YE 0.8822
104 22T 0.8822
105 IGP 0.8820
106 OUG 0.8819
107 KWV 0.8816
108 PW5 0.8815
109 7EH 0.8815
110 EYM 0.8809
111 BZM 0.8809
112 L07 0.8809
113 4CN 0.8802
114 6XR 0.8801
115 D80 0.8801
116 D5F 0.8799
117 IPL 0.8798
118 QNM 0.8797
119 RPN 0.8795
120 D87 0.8793
121 HA6 0.8793
122 1Q4 0.8792
123 0DJ 0.8792
124 AZY 0.8790
125 PB2 0.8788
126 AP6 0.8787
127 H35 0.8781
128 0QV 0.8781
129 GJE 0.8778
130 XG1 0.8778
131 3SU 0.8777
132 AC2 0.8776
133 SCE 0.8773
134 ML1 0.8772
135 52F 0.8770
136 6XC 0.8769
137 MPU 0.8769
138 A6Z 0.8769
139 BP5 0.8766
140 GJW 0.8764
141 5EZ 0.8763
142 4AU 0.8763
143 9JT 0.8760
144 Z25 0.8760
145 EEK 0.8759
146 P9L 0.8759
147 TEF 0.8759
148 FZ6 0.8758
149 HHB 0.8758
150 0QA 0.8757
151 M5A 0.8757
152 TCT 0.8756
153 CX5 0.8753
154 0SX 0.8751
155 M62 0.8747
156 0DF 0.8745
157 MQR 0.8743
158 A05 0.8743
159 OUA 0.8743
160 IJ4 0.8741
161 TMP 0.8739
162 NY4 0.8733
163 T21 0.8732
164 109 0.8731
165 CHV 0.8729
166 2QU 0.8728
167 F21 0.8725
168 JCL 0.8724
169 0J2 0.8723
170 TRP 0.8721
171 EYJ 0.8718
172 RYY 0.8718
173 2L2 0.8717
174 B4L 0.8716
175 797 0.8713
176 1AJ 0.8712
177 2L1 0.8708
178 3CX 0.8707
179 JP8 0.8705
180 B5A 0.8705
181 NEO 0.8700
182 1OT 0.8700
183 DDC 0.8696
184 HGK 0.8694
185 7PS 0.8693
186 RZ0 0.8692
187 6U5 0.8691
188 0XR 0.8691
189 7PJ 0.8687
190 S0A 0.8685
191 LVB 0.8681
192 7ZO 0.8678
193 NVS 0.8671
194 OT4 0.8670
195 41L 0.8666
196 K7H 0.8666
197 GVI 0.8664
198 0HZ 0.8664
199 GHQ 0.8663
200 BIO 0.8661
201 RYJ 0.8659
202 H4B 0.8659
203 JTF 0.8653
204 HKK 0.8646
205 SNV 0.8646
206 5KN 0.8645
207 L02 0.8641
208 536 0.8640
209 HPX 0.8640
210 3N0 0.8638
211 SVG 0.8635
212 A8D 0.8634
213 JWW 0.8632
214 JF5 0.8631
215 DOC 0.8627
216 5F1 0.8626
217 20P 0.8624
218 NXB 0.8623
219 68Y 0.8621
220 3WK 0.8621
221 ADL 0.8619
222 BUX 0.8616
223 8Y7 0.8616
224 T5J 0.8614
225 2OX 0.8613
226 JYN 0.8612
227 2UD 0.8609
228 HDI 0.8607
229 PFT 0.8607
230 EXP 0.8606
231 CHJ 0.8606
232 MKN 0.8597
233 TRP GLY 0.8596
234 ENN 0.8594
235 XYP XYP 0.8592
236 7L4 0.8592
237 BMC 0.8591
238 JGY 0.8590
239 1XS 0.8584
240 G8V 0.8579
241 ZIP 0.8578
242 14N 0.8577
243 PNX 0.8571
244 2QV 0.8569
245 9ME 0.8562
246 LR2 0.8559
247 SNJ 0.8552
248 EUH 0.8552
249 13F 0.8547
250 PTB 0.8537
251 O9Q 0.8532
252 IMH 0.8527
253 9PP 0.8509
Ligand no: 2; 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
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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