Receptor
PDB id Resolution Class Description Source Keywords
1DG5 2 Å EC: 1.5.1.3 DIHYDROFOLATE REDUCTASE OF MYCOBACTERIUM TUBERCULOSIS COMPLE NADPH AND TRIMETHOPRIM MYCOBACTERIUM TUBERCULOSIS DIHYDROFOLATE REDUCTASE STRUCTURE-BASED INHIBITOR DESIGN FOLATEANALOGS ROSSMANN FOLD NICOTINAMIDE ADENINE DINUCLEOTRIMETHOPRIM TUBERCULOSIS OXIDOREDUCTASE
Ref.: THREE-DIMENSIONAL STRUCTURE OF M. TUBERCULOSIS DIHY REDUCTASE REVEALS OPPORTUNITIES FOR THE DESIGN OF N TUBERCULOSIS DRUGS. J.MOL.BIOL. V. 295 307 2000
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:202;
A:203;
A:204;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NDP A:200;
Valid;
none;
submit data
745.421 C21 H30 N7 O17 P3 c1nc(...
TOP A:201;
Valid;
none;
Ki = 88 uM
290.318 C14 H18 N4 O3 COc1c...
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: NDP; Similar ligands found: 180
No: Ligand ECFP6 Tc MDL keys Tc
1 NDP 1 1
2 0WD 0.827273 1
3 NAI 0.803738 0.986842
4 NMN AMP PO4 0.794643 0.948052
5 NPW 0.692308 0.962025
6 NZQ 0.686441 0.987013
7 1DG 0.68 1
8 DG1 0.68 1
9 A2R 0.650943 0.909091
10 A22 0.64486 0.934211
11 TXP 0.644628 0.924051
12 ATR 0.640777 0.894737
13 NA7 0.636364 0.886076
14 XNP 0.620968 0.949367
15 AP0 0.598361 0.948718
16 A2P 0.598039 0.881579
17 NJP 0.574803 0.923077
18 25L 0.550847 0.934211
19 ODP 0.550388 0.936709
20 NAX 0.544 0.949367
21 25A 0.53913 0.921053
22 80F 0.537879 0.914634
23 2AM 0.529412 0.87013
24 NDP DTT 0.528169 0.891566
25 6V0 0.519685 0.974026
26 NAP 0.514493 0.922078
27 7L1 0.507143 0.763441
28 EAD 0.507143 0.949367
29 A2D 0.504673 0.921053
30 TXE 0.503876 0.935897
31 NA0 0.496454 0.910256
32 TXD 0.496124 0.911392
33 AGS 0.495575 0.875
34 P1H 0.493056 0.925926
35 CO7 0.489796 0.791209
36 TAP 0.489362 0.864198
37 HQG 0.483051 0.909091
38 PAP 0.482456 0.907895
39 BA3 0.481818 0.921053
40 NAJ PZO 0.478261 0.924051
41 ATP 0.477876 0.921053
42 HEJ 0.477876 0.921053
43 B4P 0.477477 0.921053
44 AP5 0.477477 0.921053
45 ADP 0.477477 0.921053
46 OAD 0.47541 0.897436
47 5FA 0.473684 0.921053
48 APR 0.473684 0.896104
49 AR6 0.473684 0.896104
50 AQP 0.473684 0.921053
51 AN2 0.473214 0.909091
52 3OD 0.467742 0.897436
53 50T 0.464912 0.884615
54 NAJ PYZ 0.464789 0.879518
55 9X8 0.463415 0.851852
56 PO4 PO4 A A A A PO4 0.463415 0.857143
57 V3L 0.461538 0.896104
58 2A5 0.46087 0.85
59 AT4 0.460177 0.886076
60 ADQ 0.459016 0.897436
61 4AD 0.459016 0.875
62 A1R 0.459016 0.841463
63 OVE 0.458716 0.8375
64 OMR 0.458647 0.813953
65 PPS 0.457627 0.811765
66 AD9 0.456897 0.897436
67 CA0 0.45614 0.897436
68 M33 0.45614 0.884615
69 ADJ 0.455882 0.879518
70 A3P 0.455357 0.894737
71 KG4 0.452174 0.897436
72 ACP 0.452174 0.897436
73 ENP 0.451613 0.85
74 UP5 0.451128 0.948052
75 SRP 0.45 0.8625
76 ACQ 0.449153 0.897436
77 ANP 0.449153 0.897436
78 PRX 0.448276 0.82716
79 A3R 0.447154 0.841463
80 5AL 0.445378 0.884615
81 KMQ 0.445312 0.886076
82 7D4 0.443478 0.8375
83 ADX 0.443478 0.811765
84 8LQ 0.442623 0.8625
85 8LH 0.438017 0.8625
86 6YZ 0.438017 0.897436
87 A 0.436364 0.894737
88 AMP 0.436364 0.894737
89 4TC 0.433824 0.924051
90 7D3 0.433628 0.8375
91 DCA 0.433566 0.788889
92 ETB 0.433566 0.797753
93 8LE 0.433333 0.851852
94 1ZZ 0.433071 0.802326
95 BIS 0.433071 0.864198
96 JNT 0.432 0.873418
97 00A 0.432 0.864198
98 QA7 0.430894 0.851852
99 ATF 0.429752 0.886076
100 DQV 0.428571 0.934211
101 0T1 0.427586 0.788889
102 8QN 0.427419 0.884615
103 5SV 0.427419 0.788235
104 3AM 0.427273 0.857143
105 N01 0.426573 0.884615
106 LAD 0.425197 0.821429
107 WAQ 0.425197 0.841463
108 PR8 0.425197 0.811765
109 DTP 0.425 0.8375
110 PAJ 0.424 0.843373
111 AMO 0.424 0.886076
112 APC 0.423729 0.886076
113 UPA 0.423358 0.935897
114 48N 0.422222 0.853659
115 PTJ 0.421875 0.853659
116 FYA 0.421875 0.860759
117 CNA 0.421429 0.910256
118 PUA 0.42069 0.9125
119 DND 0.419118 0.910256
120 AV2 0.418033 0.848101
121 COA 0.417808 0.788889
122 3UK 0.417323 0.897436
123 OOB 0.416 0.909091
124 IVC 0.415584 0.78022
125 DAT 0.415254 0.8375
126 NDO 0.414966 0.897436
127 139 0.414286 0.901235
128 B5V 0.414062 0.886076
129 TAT 0.413223 0.886076
130 3AT 0.413223 0.896104
131 T99 0.413223 0.886076
132 L3W 0.413043 0.960526
133 YLB 0.413043 0.784091
134 62F 0.4125 0.823529
135 45A 0.412281 0.848101
136 ABM 0.412281 0.848101
137 B5M 0.412214 0.875
138 YLP 0.411765 0.784091
139 ME8 0.410853 0.802326
140 NB8 0.410853 0.853659
141 SON 0.410256 0.886076
142 DLL 0.409449 0.909091
143 AHX 0.409449 0.853659
144 COS 0.409396 0.771739
145 AMX 0.409396 0.797753
146 CAO 0.409396 0.763441
147 30N 0.409396 0.72449
148 7D5 0.409091 0.8125
149 4UW 0.408759 0.9125
150 F2R 0.408451 0.825581
151 APX 0.407692 0.841463
152 AMP MG 0.40708 0.857143
153 SRA 0.40708 0.85
154 SCO 0.406667 0.788889
155 CMX 0.406667 0.788889
156 TYM 0.405797 0.886076
157 COD 0.405594 0.777778
158 OXK 0.405229 0.771739
159 CA6 0.405229 0.70297
160 AP2 0.405172 0.886076
161 A12 0.405172 0.886076
162 OZV 0.404762 0.896104
163 9SN 0.40458 0.853659
164 LAQ 0.404412 0.802326
165 T5A 0.404255 0.914634
166 FCX 0.403974 0.763441
167 FAM 0.403974 0.771739
168 ACO 0.403974 0.763441
169 CUU 0.403361 0.896104
170 YLC 0.402878 0.823529
171 1VU 0.402597 0.763441
172 B5Y 0.401515 0.875
173 FA5 0.401515 0.886076
174 HAX 0.401316 0.771739
175 CAJ 0.4 0.771739
176 AR6 AR6 0.4 0.871795
177 TXA 0.4 0.886076
178 APU 0.4 0.923077
179 4UU 0.4 0.948052
180 AFH 0.4 0.843373
Ligand no: 2; Ligand: TOP; Similar ligands found: 13
No: Ligand ECFP6 Tc MDL keys Tc
1 TOP 1 1
2 KUP 0.607143 0.93617
3 DH3 0.540541 0.807018
4 MUJ 0.492754 0.918367
5 31I 0.421053 0.730159
6 XCF 0.417722 0.886792
7 I2H 0.417722 0.886792
8 R0Y 0.416667 0.707692
9 OWM 0.416667 0.707692
10 OWS 0.401961 0.730159
11 53I 0.4 0.707692
12 53J 0.4 0.707692
13 RAR 0.4 0.69697
Similar Ligands (3D)
Ligand no: 1; Ligand: NDP; Similar ligands found: 6
No: Ligand Similarity coefficient
1 NAD 0.9403
2 NHD 0.9199
3 NAJ 0.9080
4 A3D 0.9036
5 8ID 0.8925
6 NAE 0.8727
Ligand no: 2; Ligand: TOP; Similar ligands found: 158
No: Ligand Similarity coefficient
1 4P8 0.9347
2 LI4 0.9250
3 LVE 0.9203
4 KTM 0.9186
5 5AV 0.9175
6 TCW 0.9175
7 ON1 0.9144
8 NOJ BGC 0.9129
9 QC1 0.9083
10 1OX 0.9073
11 INI 0.9055
12 DGO Z61 0.9050
13 4VT 0.9049
14 AEY 0.9046
15 P1Y 0.9034
16 PU2 0.9022
17 JE7 0.9013
18 MG7 0.9008
19 LJ4 0.8980
20 DS8 0.8946
21 Q11 0.8937
22 6LW AHR 0.8935
23 CJZ 0.8928
24 TYP 0.8921
25 0RU 0.8920
26 4JV 0.8920
27 F9W 0.8919
28 E3Y 0.8918
29 4Y2 0.8913
30 AHR AHR 0.8909
31 DE7 0.8908
32 GLC GLA 0.8900
33 E44 0.8889
34 EMU 0.8883
35 1Q4 0.8883
36 6XC 0.8862
37 50Q 0.8857
38 F0C 0.8850
39 M23 0.8848
40 7XX 0.8848
41 6UW 0.8847
42 QRP 0.8845
43 BK1 0.8845
44 D2M 0.8842
45 4L2 0.8840
46 S0I 0.8839
47 GLC IFM 0.8837
48 Z2T 0.8833
49 EDG AHR 0.8830
50 HO4 0.8829
51 A4V 0.8827
52 GMP 0.8826
53 C5Q 0.8826
54 LVB 0.8821
55 5ID 0.8821
56 MGI 0.8815
57 HA6 0.8815
58 89U 0.8810
59 12R 0.8809
60 2FA 0.8807
61 69K 0.8803
62 I0D 0.8803
63 BC3 0.8802
64 C3G 0.8798
65 AX4 0.8797
66 SCE 0.8796
67 27M 0.8794
68 WCU 0.8793
69 PCG 0.8786
70 IMK 0.8786
71 M0Y 0.8786
72 8MF 0.8784
73 94M 0.8778
74 QRQ 0.8766
75 XYP XIM 0.8762
76 FVV 0.8760
77 5R9 0.8754
78 XYP XYP 0.8745
79 5F7 0.8743
80 GLC BGC 0.8742
81 43F 0.8737
82 35G 0.8734
83 2H4 0.8731
84 GLA BEZ 0.8731
85 JA3 0.8728
86 XYS XYS 0.8725
87 TQ4 0.8715
88 7WD 0.8714
89 CMP 0.8711
90 FGQ 0.8710
91 FYJ 0.8709
92 XDH 0.8706
93 HAJ 0.8694
94 GLA GAL 0.8694
95 ADN 0.8694
96 YX0 0.8694
97 147 0.8693
98 GLC GLC 0.8693
99 MAN IFM 0.8686
100 1TD 0.8683
101 XYP XYS 0.8681
102 GLC 7LQ 0.8678
103 9W7 0.8677
104 GDQ GLC 0.8677
105 IWH 0.8675
106 BGC BGC 0.8673
107 FLF 0.8670
108 2L2 0.8668
109 BGC GLC 0.8668
110 6SZ 0.8667
111 3N3 0.8667
112 7W7 0.8664
113 EZB 0.8662
114 GAT 0.8658
115 4EU 0.8657
116 3AK 0.8655
117 AJ6 0.8650
118 BIE 0.8648
119 VIB 0.8646
120 7VF 0.8646
121 5I5 0.8645
122 D5F 0.8644
123 IM4 0.8644
124 NIP 0.8640
125 T62 0.8635
126 53X 0.8633
127 AX8 0.8631
128 YUG 0.8630
129 BMA GLA 0.8630
130 DX6 0.8625
131 NXB 0.8624
132 LOX XYP 0.8623
133 ZT2 0.8620
134 4KN 0.8619
135 FL9 0.8618
136 KS5 0.8617
137 WL3 0.8616
138 TCL 0.8613
139 LRT 0.8609
140 6BD 0.8604
141 1JF 0.8602
142 N22 0.8602
143 6SW 0.8596
144 XDI 0.8591
145 PFT 0.8590
146 CHJ 0.8582
147 DZ1 0.8571
148 RNK 0.8570
149 D2S 0.8565
150 HZ8 0.8563
151 340 0.8555
152 EUN 0.8547
153 QTS 0.8543
154 51P 0.8538
155 SP1 0.8535
156 IKY 0.8529
157 9MR 0.8516
158 NWL 0.8516
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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