Receptor
PDB id Resolution Class Description Source Keywords
3e3u 1.56 Å EC: 3.5.1.88 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PEPTIDE DEFORMYLASE IN COMPLEX WITH INHIBITOR MYCOBACTERIUM TUBERCULOSIS METALLO-ENZYME HYDROLASE IRON METAL-BINDING PROTEIN BIOSYNTHESIS
Ref.: PEPTIDE DEFORMYLASE INHIBITORS OF MYCOBACTERIUM TUBERCULOSIS: SYNTHESIS, STRUCTURAL INVESTIGATIONS, AND BIOLOGICAL RESULTS. BIOORG.MED.CHEM.LETT. V. 18 6568 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NI A:200;
Part of Protein;
none;
submit data
58.693 Ni [Ni+2...
NVC A:201;
A:202;
A:203;
Valid;
Valid;
Valid;
none;
none;
none;
ic50 = 0.013 uM
359.42 C19 H25 N3 O4 CCCC[...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3E3U 1.56 Å EC: 3.5.1.88 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PEPTIDE DEFORMYLASE IN COMPLEX WITH INHIBITOR MYCOBACTERIUM TUBERCULOSIS METALLO-ENZYME HYDROLASE IRON METAL-BINDING PROTEIN BIOSYNTHESIS
Ref.: PEPTIDE DEFORMYLASE INHIBITORS OF MYCOBACTERIUM TUBERCULOSIS: SYNTHESIS, STRUCTURAL INVESTIGATIONS, AND BIOLOGICAL RESULTS. BIOORG.MED.CHEM.LETT. V. 18 6568 2008
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 3E3U ic50 = 0.013 uM NVC C19 H25 N3 O4 CCCC[C@H](....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 3E3U ic50 = 0.013 uM NVC C19 H25 N3 O4 CCCC[C@H](....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3E3U ic50 = 0.013 uM NVC C19 H25 N3 O4 CCCC[C@H](....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NVC; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 NVC 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3E3U; Ligand: NVC; Similar sites found: 175
This union binding pocket(no: 1) in the query (biounit: 3e3u.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3OKI OKI 0.01036 0.4284 None
2 2GBB CIT 0.001029 0.42195 None
3 4RHP PEF 0.003764 0.41927 1.01523
4 5K52 OCD 0.006524 0.41612 1.01523
5 1ZDT PEF 0.0179 0.40307 1.01523
6 3SE5 ANP 0.002397 0.42817 1.21951
7 2XXP DSL 0.02024 0.43204 1.52284
8 5G3N X28 0.009244 0.40906 1.5748
9 2FV5 541 0.000002686 0.59117 2.03046
10 1BKC INN 0.000006389 0.53109 2.03046
11 3LL5 ADP 0.01461 0.41583 2.03046
12 1T27 PCW 0.03782 0.40195 2.03046
13 1BWO LPC 0.001224 0.44586 2.22222
14 2J83 BAT 0.00002473 0.52616 2.53807
15 5B4B LP5 0.008853 0.42043 2.53807
16 2E2R 2OH 0.01366 0.41728 2.53807
17 4NTC FAD 0.02024 0.41569 2.53807
18 2A8X FAD 0.02414 0.41354 2.53807
19 3KH5 AMP 0.0321 0.41116 2.53807
20 5AAV GW5 0.03924 0.40945 2.53807
21 4COL DTP 0.006858 0.40744 2.53807
22 4P42 PEE 0.01463 0.40444 2.53807
23 4TV1 36M 0.001765 0.40434 2.53807
24 2PZM NAD 0.03665 0.40431 2.53807
25 2PZM UDP 0.03665 0.40431 2.53807
26 2BJ4 OHT 0.01162 0.4027 2.53807
27 3KJS DQ1 0.03735 0.40136 2.53807
28 1AOE GW3 0.02439 0.4098 2.60417
29 2W14 WR2 0.00001634 0.52339 3.04569
30 1KAP GLY SER ASN SER 0.0004908 0.4487 3.04569
31 2EVL GAL SPH EIC 0.03335 0.41174 3.04569
32 2YG3 FAD 0.02555 0.4097 3.04569
33 3KC1 2T6 0.008758 0.40656 3.04569
34 1ZMD FAD 0.03281 0.40593 3.04569
35 1ZVX FIN 0.0001742 0.50994 3.06748
36 5CSD ACD 0.03057 0.40394 3.14465
37 1UVC STE 0.01892 0.40323 3.2967
38 2TCL RO4 0.00003186 0.52109 3.5503
39 2ZXG S23 0.00004464 0.52513 3.5533
40 4WKI 3PW 0.00003752 0.49803 3.5533
41 4CA5 3EF 0.002461 0.46812 3.5533
42 3DBK RDF 0.001573 0.44085 3.5533
43 3KDU NKS 0.01796 0.41453 3.5533
44 2C7G FAD 0.04319 0.40858 3.5533
45 2C7G ODP 0.0451 0.40694 3.5533
46 3LU1 NAD 0.01945 0.40636 3.5533
47 5NJI 8Z2 0.01579 0.40569 3.5533
48 3ET1 ET1 0.009294 0.40537 3.5533
49 4B7P 9UN 0.03632 0.40532 3.5533
50 2Q0L FAD 0.03749 0.40214 3.5533
51 5V4R MGT 0.00002846 0.54916 3.7037
52 3ZVS MLI 0.000607 0.42737 3.75
53 3G08 FEE 0.04135 0.40758 4.0404
54 4ZW3 4S9 0.00003693 0.54283 4.06091
55 4BXK 1IU 0.00146 0.46727 4.06091
56 4OYA 1VE 0.02103 0.42817 4.06091
57 5BYZ 4WE 0.007687 0.42469 4.06091
58 2OBD PCW 0.008062 0.42369 4.06091
59 3Q8G PEE 0.04798 0.4042 4.06091
60 5KDS A2G THR ALA PRO GLY GLY NAG SIA 0.008307 0.40365 4.06091
61 1FBL HTA 0.00004529 0.4877 4.56853
62 4AR8 IP8 GLY PRO ALA 0.00005677 0.48756 4.56853
63 3EE4 MYR 0.004581 0.42326 4.56853
64 3WDM ADN 0.01977 0.40716 4.56853
65 1PZO CBT 0.03297 0.40229 4.56853
66 5OCA 9QZ 0.00172 0.47351 4.62185
67 2AX9 BHM 0.01746 0.41708 5.07614
68 5A0R ACE GLU VAL ASN PRO 0.01191 0.41155 5.07614
69 3D3X ARG ILE MET GLU NH2 0.00909 0.41108 5.07614
70 2GMH FAD 0.03146 0.41086 5.07614
71 5JCA FAD 0.02992 0.40797 5.07614
72 2GMH UQ5 0.011 0.4072 5.07614
73 1ZDU P3A 0.01469 0.4058 5.07614
74 3NFD COA 0.01135 0.4075 5.22876
75 4IGH ORO 0.03414 0.41827 5.58376
76 4IGH FMN 0.03414 0.41827 5.58376
77 4IGH 1EA 0.03414 0.41827 5.58376
78 5L7G 6QE 0.008899 0.41151 5.58376
79 2A3I C0R 0.009111 0.40936 5.58376
80 2B9W FAD 0.0438 0.40826 5.58376
81 4LY9 1YY 0.03542 0.40667 5.58376
82 4LY9 S6P 0.03418 0.40667 5.58376
83 4H6Q TFB 0.01828 0.40524 5.58376
84 3DWB RDF 0.006455 0.40065 5.58376
85 3IQE F42 0.02548 0.40062 5.58376
86 1MMQ RRS 0.00001944 0.52576 5.88235
87 4P8O 883 0.01481 0.40187 5.88235
88 4NJS G08 0.02502 0.40101 6.06061
89 1YP1 LYS ASN LEU 0.000004083 0.50368 6.09137
90 4QHP 32Q 0.0006707 0.46204 6.09137
91 1SR7 MOF 0.01113 0.41816 6.09137
92 4ZBR DIF 0.01329 0.41559 6.09137
93 3GDH SAH 0.01554 0.4032 6.09137
94 4PJT 2YQ 0.02457 0.40023 6.09137
95 5C2N NAG 0.0206 0.40031 6.25
96 3Q2H QHF 0.00001177 0.53844 6.59898
97 3HBV ALA LYS ALA SER GLN ALA ALA 0.00005467 0.49055 6.59898
98 1R55 097 0.00002007 0.48947 6.59898
99 3DLG GWE 0.01493 0.43531 6.59898
100 3SQP 3J8 0.01502 0.41069 6.59898
101 3T6E UQ9 0.02537 0.40606 6.59898
102 3PVT 3HC 0.02965 0.40366 6.59898
103 3KFC 61X 0.02247 0.40211 6.59898
104 4WZV E40 0.00006247 0.51626 6.875
105 1HFS L04 0.0001264 0.51378 6.875
106 1ATL 0QI 0.000003786 0.56892 7.1066
107 4RW3 TDA 0.003374 0.44079 7.1066
108 4WB6 ATP 0.01166 0.41057 7.1066
109 5IF4 6AK 0.01722 0.40521 7.54717
110 2ALG HP6 0.007279 0.4139 7.6087
111 2ALG DAO 0.007279 0.4139 7.6087
112 3HY9 098 0.000007183 0.54828 7.61421
113 4GAA BES 0.00007638 0.49602 7.61421
114 3ET3 ET1 0.009045 0.40775 7.61421
115 3T03 3T0 0.006778 0.40767 7.61421
116 1SB8 NAD 0.0365 0.40753 7.61421
117 2HFP NSI 0.01274 0.40578 7.61421
118 3E1T FAD 0.03978 0.40249 7.61421
119 4CQB MLI 0.01869 0.40219 7.61421
120 5DCH 1YO 0.007948 0.42267 7.8125
121 4DV8 0LX 0.0000814 0.52607 8.12183
122 2VJ8 HA2 0.0001621 0.51807 8.12183
123 3H0A D30 0.007797 0.42034 8.12183
124 1H0H MGD 0.03069 0.40194 8.12183
125 4POJ 2VP 0.01677 0.40014 8.12183
126 2B96 ANN 0.01197 0.40383 8.13008
127 1HN4 MJI 0.02212 0.42823 8.39695
128 4IN9 SER TRP PHE PRO 0.0004778 0.40983 8.43373
129 3C3N FMN 0.01716 0.41346 8.62944
130 4E2J MOF 0.008727 0.41191 8.62944
131 4P6X HCY 0.00958 0.40659 8.62944
132 3BQD DAY 0.01196 0.40384 8.62944
133 4LSJ LSJ 0.01381 0.40092 8.62944
134 3HUJ AGH 0.042 0.40287 9.09091
135 3AHO 3A2 0.002138 0.44393 9.13706
136 4UCC ZKW 0.0142 0.42484 9.13706
137 3WCA FPS 0.01434 0.41034 9.13706
138 2XQ0 BES 0.0002156 0.44701 9.64467
139 3R9V DXC 0.0002684 0.42885 9.64467
140 3PE2 E1B 0.02771 0.4105 9.64467
141 4GBD MCF 0.01051 0.40645 9.64467
142 1N8V BDD 0.021 0.40588 9.82143
143 1RM8 BAT 0.00007512 0.46042 10.0592
144 4DD8 BAT 0.00001217 0.48659 10.1523
145 4ARF IP8 GLY PRO ALA 0.0003681 0.46507 10.1523
146 1QJI PKF 0.0064 0.4088 10.5
147 4AIG FLX 0.00002966 0.4919 10.6599
148 3DST GRG 0.01506 0.44164 10.6599
149 2Q1H AS4 0.007852 0.40875 10.6599
150 4KWD JF2 0.01714 0.40118 10.6599
151 4RC8 STE 0.005185 0.4225 11.1675
152 3G4G D71 0.01135 0.40136 11.1675
153 1KUK PCA LYS TRP 0.00005215 0.49209 11.6751
154 2A1L PCW 0.01809 0.41903 11.6751
155 2ZCQ B65 0.03605 0.40385 11.6751
156 4KX8 L2O VAL VAL ASP 0.0001679 0.48776 12.6904
157 1Q3A NGH 0.00004431 0.47927 13.3333
158 3CXH SMA 0.01119 0.41285 13.3929
159 2DYR PGV 0.02612 0.40544 14.2857
160 4B52 RDF 0.002016 0.42924 15.2284
161 1OFD AKG 0.01114 0.4205 15.2284
162 1OFD FMN 0.01236 0.4205 15.2284
163 2J8C U10 0.04498 0.4119 15.2284
164 2J8C SPO 0.04498 0.4119 15.2284
165 3WV1 WHH 0.0004009 0.50087 16.3743
166 3G58 988 0.003568 0.40618 17.7665
167 2QZT PLM 0.006598 0.42521 18.018
168 3GWT 066 0.01461 0.41241 20.3046
169 2R4J FAD 0.01171 0.43593 24.3655
170 2R4J 13P 0.01171 0.43593 24.3655
171 1EZV SMA 0.01108 0.41305 30.9091
172 1RL4 BRR 0.00000000001556 0.71196 42.5532
173 3GN8 DEX 0.004904 0.42006 42.8571
174 1M2Z DEX 0.0124 0.40138 42.8571
175 3UWB BB2 0.0000000002191 0.76666 49.3507
Pocket No.: 2; Query (leader) PDB : 3E3U; Ligand: NVC; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3e3u.bio1) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3E3U; Ligand: NVC; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3e3u.bio1) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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