Receptor
PDB id Resolution Class Description Source Keywords
1DF7 1.7 Å EC: 1.5.1.3 DIHYDROFOLATE REDUCTASE OF MYCOBACTERIUM TUBERCULOSIS COMPLE NADPH AND METHOTREXATE MYCOBACTERIUM TUBERCULOSIS DIHYDROFOLATE REDUCTASE STRUCTURE-BASED INHIBITOR DESIGN FOLATEANALOGS ROSSMANN FOLD NICOTINAMIDE ADENINE DINUCLEOMETHOTREXATE 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:502;
A:503;
A:504;
A:505;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
MTX A:501;
Valid;
none;
Ki = 11 nM
454.439 C20 H22 N8 O5 CN(Cc...
NDP A:500;
Valid;
none;
submit data
745.421 C21 H30 N7 O17 P3 c1nc(...
SO4 A:506;
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 INHIBITED BY THE ACYCLIC 4R ISOMER OF INH-NADP A D ERIVATIVE OF THE PRODRUG ISONIAZID. MYCOBACTERIUM TUBERCULOSIS NADP ISONIAZID REDUCTASE INHIBITOR BISUBSTRATE TUBERCULOSIS OXIDOREDUCTASE ONE-CARBON METABOLISM
Ref.: MYCOBACTERIUM TUBERCULOSIS DIHYDROFOLATE REDUCTASE IS A TARGET FOR ISONIAZID NAT.STRUCT.MOL.BIOL. V. 13 408 2006
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 28 families.
1 2CIG Ki = 1 nM 1DG C27 H33 N8 O18 P3 c1cnccc1C(....
2 1DG8 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
3 1DG5 Ki = 88 uM TOP C14 H18 N4 O3 COc1cc(cc(....
4 1DF7 Ki = 11 nM MTX C20 H22 N8 O5 CN(Cc1cnc2....
5 5JA3 ic50 = 173 nM U06 C23 H22 N4 O3 CCc1c(c(nc....
6 1DG7 Ki = 187 nM WRB C14 H20 Br N5 O2 CC1(N=C(N=....
70% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 4KL9 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 4KNE Kd = 1.26 uM 1CY C11 H14 Cl N5 CC1(N=C(N=....
3 4KM2 Kd = 0.82 uM TOP C14 H18 N4 O3 COc1cc(cc(....
4 4KLX - ATR C10 H16 N5 O13 P3 c1nc(c2c(n....
5 4KM0 Kd = 0.91 uM CP6 C12 H13 Cl N4 CCc1c(c(nc....
6 2CIG Ki = 1 nM 1DG C27 H33 N8 O18 P3 c1cnccc1C(....
7 1DG8 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
8 1DG5 Ki = 88 uM TOP C14 H18 N4 O3 COc1cc(cc(....
9 1DF7 Ki = 11 nM MTX C20 H22 N8 O5 CN(Cc1cnc2....
10 5JA3 ic50 = 173 nM U06 C23 H22 N4 O3 CCc1c(c(nc....
11 1DG7 Ki = 187 nM WRB C14 H20 Br N5 O2 CC1(N=C(N=....
50% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 12 families.
1 4KL9 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 4KNE Kd = 1.26 uM 1CY C11 H14 Cl N5 CC1(N=C(N=....
3 4KM2 Kd = 0.82 uM TOP C14 H18 N4 O3 COc1cc(cc(....
4 4KLX - ATR C10 H16 N5 O13 P3 c1nc(c2c(n....
5 4KM0 Kd = 0.91 uM CP6 C12 H13 Cl N4 CCc1c(c(nc....
6 2CIG Ki = 1 nM 1DG C27 H33 N8 O18 P3 c1cnccc1C(....
7 1DG8 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
8 1DG5 Ki = 88 uM TOP C14 H18 N4 O3 COc1cc(cc(....
9 1DF7 Ki = 11 nM MTX C20 H22 N8 O5 CN(Cc1cnc2....
10 5JA3 ic50 = 173 nM U06 C23 H22 N4 O3 CCc1c(c(nc....
11 1DG7 Ki = 187 nM WRB C14 H20 Br N5 O2 CC1(N=C(N=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MTX; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 MTX 1 1
2 3BI 0.783505 0.884058
3 2MX 0.778947 0.924242
4 04J 0.663043 0.870968
5 MT1 0.632653 0.968254
6 MOT 0.534653 0.923077
7 COP 0.453782 0.815385
8 FOL 0.410714 0.779412
Ligand no: 2; Ligand: NDP; Similar ligands found: 159
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 DG1 0.68 1
8 1DG 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 2AM 0.529412 0.87013
23 6V0 0.519685 0.974026
24 NAP 0.514493 0.922078
25 EAD 0.507143 0.949367
26 A2D 0.504673 0.921053
27 TXE 0.503876 0.935897
28 NA0 0.496454 0.910256
29 TXD 0.496124 0.911392
30 SAP 0.495575 0.875
31 AGS 0.495575 0.875
32 P1H 0.493056 0.925926
33 CO7 0.489796 0.791209
34 TAP 0.489362 0.864198
35 PAP 0.482456 0.907895
36 BA3 0.481818 0.921053
37 NAJ PZO 0.478261 0.924051
38 ATP 0.477876 0.921053
39 B4P 0.477477 0.921053
40 ADP 0.477477 0.921053
41 AP5 0.477477 0.921053
42 OAD 0.47541 0.897436
43 5FA 0.473684 0.921053
44 AR6 0.473684 0.896104
45 APR 0.473684 0.896104
46 AQP 0.473684 0.921053
47 AN2 0.473214 0.909091
48 3OD 0.467742 0.897436
49 50T 0.464912 0.884615
50 PO4 PO4 A A A A PO4 0.463415 0.857143
51 V3L 0.461538 0.896104
52 2A5 0.46087 0.85
53 A1R 0.459016 0.841463
54 ADQ 0.459016 0.897436
55 4AD 0.459016 0.875
56 OVE 0.458716 0.8375
57 OMR 0.458647 0.813953
58 PPS 0.457627 0.811765
59 AD9 0.456897 0.897436
60 CA0 0.45614 0.897436
61 M33 0.45614 0.884615
62 ADJ 0.455882 0.879518
63 A3P 0.455357 0.894737
64 ACP 0.452174 0.897436
65 ENP 0.451613 0.85
66 UP5 0.451128 0.948052
67 SRP 0.45 0.8625
68 ANP 0.449153 0.897436
69 ACQ 0.449153 0.897436
70 PRX 0.448276 0.82716
71 5AL 0.445378 0.884615
72 7D4 0.443478 0.8375
73 ADX 0.443478 0.811765
74 AMP 0.436364 0.894737
75 A 0.436364 0.894737
76 4TC 0.433824 0.924051
77 7D3 0.433628 0.8375
78 ETB 0.433566 0.797753
79 DCA 0.433566 0.788889
80 1ZZ 0.433071 0.802326
81 BIS 0.433071 0.864198
82 00A 0.432 0.864198
83 ATF 0.429752 0.886076
84 0T1 0.427586 0.788889
85 5SV 0.427419 0.788235
86 8QN 0.427419 0.884615
87 3AM 0.427273 0.857143
88 N01 0.426573 0.884615
89 PR8 0.425197 0.811765
90 WAQ 0.425197 0.841463
91 LAD 0.425197 0.821429
92 DTP 0.425 0.8375
93 AMO 0.424 0.886076
94 PAJ 0.424 0.843373
95 APC 0.423729 0.886076
96 UPA 0.423358 0.935897
97 48N 0.422222 0.853659
98 FYA 0.421875 0.860759
99 PTJ 0.421875 0.853659
100 CNA 0.421429 0.910256
101 PUA 0.42069 0.9125
102 NXX 0.419118 0.910256
103 DND 0.419118 0.910256
104 AV2 0.418033 0.848101
105 COA 0.417808 0.788889
106 3UK 0.417323 0.897436
107 OOB 0.416 0.909091
108 IVC 0.415584 0.78022
109 DAT 0.415254 0.8375
110 NDO 0.414966 0.897436
111 139 0.414286 0.901235
112 3AT 0.413223 0.896104
113 TAT 0.413223 0.886076
114 YLB 0.413043 0.784091
115 62F 0.4125 0.823529
116 ABM 0.412281 0.848101
117 YAP 0.412214 0.875
118 YLP 0.411765 0.784091
119 ME8 0.410853 0.802326
120 NB8 0.410853 0.853659
121 SON 0.410256 0.886076
122 DLL 0.409449 0.909091
123 AHX 0.409449 0.853659
124 COS 0.409396 0.771739
125 AMX 0.409396 0.797753
126 CAO 0.409396 0.763441
127 30N 0.409396 0.72449
128 7D5 0.409091 0.8125
129 4UW 0.408759 0.9125
130 APX 0.407692 0.841463
131 SRA 0.40708 0.85
132 CMX 0.406667 0.788889
133 SCO 0.406667 0.788889
134 TYM 0.405797 0.886076
135 COD 0.405594 0.777778
136 OXK 0.405229 0.771739
137 CA6 0.405229 0.70297
138 A12 0.405172 0.886076
139 AP2 0.405172 0.886076
140 9SN 0.40458 0.853659
141 LAQ 0.404412 0.802326
142 T5A 0.404255 0.914634
143 FAM 0.403974 0.771739
144 ACO 0.403974 0.763441
145 FCX 0.403974 0.763441
146 AMP MG 0.403509 0.825
147 VO4 ADP 0.403226 0.860759
148 ADP VO4 0.403226 0.860759
149 YLC 0.402878 0.823529
150 1VU 0.402597 0.763441
151 FA5 0.401515 0.886076
152 HAX 0.401316 0.771739
153 APU 0.4 0.923077
154 TXA 0.4 0.886076
155 A U 0.4 0.898734
156 4UU 0.4 0.948052
157 AFH 0.4 0.843373
158 CAJ 0.4 0.771739
159 AR6 AR6 0.4 0.871795
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2CIG; Ligand: 1DG; Similar sites found: 56
This union binding pocket(no: 1) in the query (biounit: 2cig.bio1) has 43 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3KO0 TFP 0.02633 0.43062 None
2 3OF1 CMP 0.01592 0.42934 None
3 3NOJ PYR 0.03762 0.42009 1.88679
4 2FKA BEF 0.006629 0.45095 2.32558
5 1NJJ ORX 0.01991 0.40178 2.51572
6 2F2U M77 0.01515 0.43046 3.14465
7 2EG5 SAH 0.03933 0.40192 3.14465
8 4MGA 27L 0.009988 0.44861 3.77358
9 4BQS K2Q 0.009865 0.44465 3.77358
10 4IF4 BEF 0.03558 0.41967 3.77358
11 2OBM ADP 0.04344 0.41867 3.77358
12 1U5R ATP 0.02214 0.40818 3.77358
13 3UUA 0CZ 0.04376 0.40605 3.77358
14 3QP6 HL6 0.03848 0.40241 3.77358
15 3BU1 HSM 0.03184 0.41432 4.05405
16 2HHP FLC 0.007119 0.49984 4.40252
17 3GQT UFO 0.0398 0.40486 4.40252
18 1D8C GLV 0.04586 0.40366 4.40252
19 2Z49 AMG 0.02195 0.42692 5.03145
20 2FFU UDP 0.02639 0.40447 5.03145
21 4UYG 73B 0.04105 0.41545 5.09554
22 3EYK EYK 0.01983 0.43129 5.66038
23 4QAR ADE 0.04169 0.40063 5.66038
24 2J5V PCA 0.02777 0.43616 6.28931
25 4UCC ZKW 0.01976 0.42543 6.28931
26 2WQN ADP 0.03088 0.41059 6.28931
27 1YBH P22 0.04312 0.40639 6.28931
28 1ZDU P3A 0.009393 0.40572 6.28931
29 3BD9 A3P 0.04688 0.40114 6.28931
30 3G2Y GF4 0.04263 0.40574 6.91824
31 2Q0L NAP 0.0341 0.40199 6.91824
32 4LRJ ANP 0.0343 0.40186 6.91824
33 2VOH CIT 0.02859 0.42525 7.00637
34 1T9D P22 0.02917 0.42325 7.54717
35 3CBG SAH 0.02727 0.40378 8.1761
36 1GEG GLC 0.008873 0.44565 8.80503
37 4HA9 NDP 0.0000006442 0.43804 8.80503
38 2NUN ADP 0.03409 0.41553 9.43396
39 1QZZ SAM 0.0302 0.40776 9.43396
40 4OAR 2S0 0.02409 0.40067 9.43396
41 2AWN ADP 0.03142 0.42302 10.0629
42 2X1E X1E 0.0289 0.41595 10.0629
43 2QJY SMA 0.01185 0.40145 10.0629
44 3B6C SDN 0.03924 0.41605 11.9497
45 2QV7 ADP 0.02275 0.41072 13.2075
46 3GCM 5GP 0.01971 0.42794 14.6341
47 5FJJ MAN 0.02316 0.42845 15.0943
48 2IYF UDP 0.01826 0.43023 18.239
49 1GXU 2HP 0.04447 0.41814 18.6813
50 2D7I UDP 0.02887 0.41211 19.4969
51 3NRR NAP 0.000000000000003553 0.78634 21.3836
52 3NRR D16 0.000000000000001554 0.75872 21.3836
53 3ITJ CIT 0.01723 0.44318 21.3836
54 5DXV NAP 0.00000000007348 0.52146 37.1795
55 4EIL FOL 0.0000000002346 0.81375 44.0252
56 4EIL NDP 0.000000000006591 0.77438 44.0252
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