Receptor
PDB id Resolution Class Description Source Keywords
6VSD 1.69 Å EC: 1.5.1.3 MYCOBACTERIUM TUBERCULOSIS DIHYDROFOLATE REDUCTASE IN COMPLE ((THIOPHEN-2-YLTHIO)METHYL)BENZOIC ACID (FRAGMENT 13) 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
CO A:203;
B:203;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
58.933 Co [Co+2...
NAP B:202;
A:202;
 Valid;
Valid;
 none;
none;
 submit data
743.405 C21 H28 N7 O17 P3 c1cc(...
JBB A:201;
B:201;
 Valid;
Valid;
 none;
none;
 Kd = 0.75 mM
250.337 C12 H10 O2 S2 c1cc(...
PO4 B:204;
 Invalid;
 none;
 submit data
94.971 O4 P [O-]P...
SO4 A:204;
 Invalid;
 none;
 submit data
96.063 O4 S [O-]S...
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: JBB; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 JBB 1 1
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: JBB; Similar ligands found: 118
No: Ligand Similarity coefficient
1 4RG 0.9585
2 NZ4 0.9563
3 6NJ 0.9430
4 MH5 0.9395
5 L12 0.9395
6 KVD 0.9270
7 T34 0.9255
8 EEY 0.9216
9 LFK 0.9211
10 UV4 0.9164
11 HWH 0.9159
12 ZEA 0.9142
13 D8I 0.9135
14 RK4 0.9109
15 LZ7 0.9106
16 GW9 0.9106
17 YIP 0.9069
18 SZA 0.9062
19 ASE 0.9060
20 NFZ 0.9053
21 8KW 0.9045
22 CMG 0.9044
23 ZIP 0.9039
24 V15 0.9024
25 QDR 0.9010
26 SCE 0.9005
27 D8Y 0.9002
28 3NM 0.8984
29 H0V 0.8976
30 AEY 0.8974
31 SE5 0.8967
32 ML1 0.8965
33 0OP 0.8963
34 WA2 0.8946
35 TVZ 0.8939
36 TVC 0.8935
37 H35 0.8932
38 F1V 0.8926
39 EMU 0.8920
40 0QA 0.8912
41 108 0.8903
42 HPK 0.8903
43 T61 0.8897
44 HHV 0.8894
45 AX5 0.8894
46 LJ1 0.8882
47 HCC 0.8879
48 U4J 0.8865
49 GOW 0.8857
50 D8B 0.8850
51 GQZ 0.8839
52 KWK 0.8839
53 F91 0.8832
54 8M5 0.8832
55 RE2 0.8827
56 RCV 0.8824
57 Z3R 0.8822
58 4YE 0.8817
59 QS4 0.8817
60 EDG AHR 0.8817
61 0RU 0.8813
62 HAN 0.8797
63 R4E 0.8791
64 JOT 0.8787
65 4YF 0.8780
66 ZYC 0.8775
67 Q5M 0.8772
68 STL 0.8771
69 UN4 0.8758
70 41L 0.8757
71 LJ2 0.8753
72 BTQ 0.8750
73 RNP 0.8743
74 D9Q 0.8742
75 43O 0.8730
76 NU3 0.8729
77 NRG 0.8728
78 BVB 0.8726
79 EBB 0.8725
80 NIY 0.8724
81 VGV 0.8722
82 5HG 0.8722
83 S8J 0.8722
84 2M7 0.8718
85 5VU 0.8715
86 C4E 0.8712
87 4K2 0.8710
88 DN8 0.8705
89 TPM 0.8703
90 U14 0.8703
91 6XC 0.8700
92 AZY 0.8686
93 STV 0.8685
94 245 0.8683
95 A05 0.8679
96 0V8 0.8669
97 JL7 0.8655
98 IJ1 0.8646
99 RE4 0.8641
100 NIP 0.8639
101 NW1 0.8638
102 M4Q 0.8638
103 U12 0.8638
104 LI7 0.8636
105 ESJ 0.8625
106 QUG 0.8618
107 Q92 0.8616
108 M62 0.8615
109 SJR 0.8595
110 JTF 0.8591
111 122 0.8562
112 FSU 0.8554
113 KTV 0.8554
114 SZ5 0.8553
115 4ZF 0.8550
116 SNP 0.8545
117 15I 0.8544
118 7G2 0.8536
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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