Receptor
PDB id Resolution Class Description Source Keywords
3PN1 2 Å EC: 6.5.1.2 NOVEL BACTERIAL NAD+-DEPENDENT DNA LIGASE INHIBITORS WITH BR SPECTRUM POTENCY AND ANTIBACTERIAL EFFICACY IN VIVO HAEMOPHILUS INFLUENZAE ATP GRASP FOLD LIGASE DNA BACTERIA LIGASE-LIGASE INHIBITCOMPLEX
Ref.: NOVEL BACTERIAL NAD+-DEPENDENT DNA LIGASE INHIBITOR BROAD-SPECTRUM ACTIVITY AND ANTIBACTERIAL EFFICACY ANTIMICROB.AGENTS CHEMOTHER. V. 55 1088 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
IVH A:319;
Valid;
none;
ic50 = 0.507 uM
355.413 C14 H21 N5 O4 S CCCCS...
IWH A:320;
Invalid;
none;
submit data
256.3 C15 H16 N2 O2 Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3PN1 2 Å EC: 6.5.1.2 NOVEL BACTERIAL NAD+-DEPENDENT DNA LIGASE INHIBITORS WITH BR SPECTRUM POTENCY AND ANTIBACTERIAL EFFICACY IN VIVO HAEMOPHILUS INFLUENZAE ATP GRASP FOLD LIGASE DNA BACTERIA LIGASE-LIGASE INHIBITCOMPLEX
Ref.: NOVEL BACTERIAL NAD+-DEPENDENT DNA LIGASE INHIBITOR BROAD-SPECTRUM ACTIVITY AND ANTIBACTERIAL EFFICACY ANTIMICROB.AGENTS CHEMOTHER. V. 55 1088 2011
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3PN1 ic50 = 0.507 uM IVH C14 H21 N5 O4 S CCCCSc1nc(....
2 4UFZ - IWH C15 H16 N2 O2 Cc1ccc(c(c....
3 3UQ8 Kd = 45 uM NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3PN1 ic50 = 0.507 uM IVH C14 H21 N5 O4 S CCCCSc1nc(....
2 4UFZ - IWH C15 H16 N2 O2 Cc1ccc(c(c....
3 3UQ8 Kd = 45 uM NAD C21 H27 N7 O14 P2 c1cc(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 2 families.
1 1TA8 - NMN C11 H16 N2 O8 P c1cc(c[n+]....
2 4LH7 ic50 = 34 uM 1X8 C9 H8 N4 O2 S c1c2c(c(cn....
3 4LH6 ic50 = 77 uM 1X7 C8 H6 Br N3 O S c1c2c(c(cn....
4 5FPO - 10L C7 H7 N3 c1cc2cn[nH....
5 5FPR - LGA C4 H5 N3 c1cnc(nc1)....
6 4CC6 ic50 = 0.23 uM L5Y C14 H12 F3 N5 O c1cncc2c1c....
7 4CC5 Kd = 38 uM L5V C6 H4 Cl N5 c1c(nc(cn1....
8 4GLW Kd = 0.8 uM 0XT C8 H10 N6 O Cc1c(nc2c(....
9 3PN1 ic50 = 0.507 uM IVH C14 H21 N5 O4 S CCCCSc1nc(....
10 4UFZ - IWH C15 H16 N2 O2 Cc1ccc(c(c....
11 3UQ8 Kd = 45 uM NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: IVH; Similar ligands found: 20
No: Ligand ECFP6 Tc MDL keys Tc
1 IVH 1 1
2 2FA 0.567568 0.805195
3 6AD 0.5 0.807229
4 6CR 0.493671 0.794872
5 XYA 0.493333 0.835616
6 ADN 0.493333 0.835616
7 RAB 0.493333 0.835616
8 MTA 0.428571 0.813333
9 MTP 0.419753 0.864865
10 3DH 0.418605 0.837838
11 26A 0.414634 0.779221
12 6MD 0.414634 0.824324
13 1DA 0.414634 0.835616
14 5N5 0.407407 0.810811
15 EP4 0.404762 0.769231
16 5CD 0.402439 0.773333
17 A4D 0.402439 0.835616
18 DSH 0.4 0.78481
19 DTA 0.4 0.75641
20 M2T 0.4 0.772152
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3PN1; Ligand: IVH; Similar sites found: 126
This union binding pocket(no: 1) in the query (biounit: 3pn1.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3AKK ADP 0.0006042 0.41802 1.25786
2 5F90 GLA GAL 0.005079 0.42779 1.28205
3 5F90 LMR 0.00839 0.4122 1.28205
4 3OFM 4B0 0.001358 0.42376 1.57233
5 4X7Q 3YR 0.001277 0.40064 1.60256
6 5AX9 4KT 0.0007696 0.408 1.62338
7 1ZX5 LFR 0.002048 0.46492 1.66667
8 4WNP 3RJ 0.002106 0.41721 1.74216
9 4BTK DTQ 0.001203 0.40739 1.88679
10 2F57 23D 0.0004466 0.43197 1.89274
11 3VOT ADP 0.0001423 0.47209 2.20126
12 2QK4 ATP 0.000268 0.47077 2.20126
13 3PTG 932 0.001798 0.43272 2.20126
14 1PK8 ATP 0.00002637 0.42017 2.20126
15 5VLQ ANP 0.01615 0.40419 2.20126
16 1AUX AGS 0.0005135 0.41856 2.2508
17 4I94 ANP 0.001518 0.40071 2.33333
18 1S68 AMP 0.0000002803 0.62555 2.40964
19 5LXC 7AA 0.001626 0.4543 2.51572
20 5C03 AGS 0.0002574 0.42595 2.51572
21 1CM8 ANP 0.001157 0.40689 2.51572
22 3UDZ ADP 0.0009056 0.40215 2.51572
23 4WOV 3SM 0.001631 0.42341 2.52366
24 4AUA 4AU 0.0002243 0.43577 2.60586
25 5DZT AMP 0.0002583 0.48498 2.83019
26 3X01 AMP 0.0007316 0.46403 2.83019
27 1Q8Y ADE 0.000625 0.45309 2.83019
28 4G17 0VN 0.0003935 0.43728 2.83019
29 2PZI AXX 0.001256 0.42166 2.83019
30 4Y0X ADP 0.001782 0.40865 2.83019
31 4OCV ANP 0.0004051 0.4078 2.83019
32 4YMJ 4EJ 0.0003633 0.4788 2.96053
33 5DA3 58V 0.00427 0.40808 3.01887
34 4BCM T7Z 0.0004624 0.46975 3.05344
35 4BCQ TJF 0.0008321 0.43759 3.05344
36 4BCN T9N 0.0008525 0.43191 3.05344
37 4CFU 2WC 0.0008692 0.4249 3.05344
38 3TY5 ADP 0.00001042 0.49901 3.14465
39 3TY5 ATP 0.0002514 0.46243 3.14465
40 1E4E ADP 0.001055 0.4 3.14465
41 1JPA ANP 0.00131 0.40621 3.20513
42 1I7L ATP 0.00007477 0.41659 3.23625
43 5IQD GNP 0.01108 0.43963 3.27869
44 5IQD RIO 0.01159 0.43963 3.27869
45 1O9U ADZ 0.00004927 0.53629 3.45912
46 5EOB 5QQ 0.001637 0.49969 3.45912
47 4XH0 ADP 0.0002387 0.4862 3.45912
48 4UAL 3FV 0.0004749 0.48589 3.45912
49 2V7O DRN 0.00111 0.44179 3.45912
50 3F7Z 34O 0.0002544 0.43121 3.45912
51 3WVR AMP 0.001126 0.41609 3.45912
52 4JR7 GNP 0.0008684 0.40462 3.45912
53 4D2S DYK 0.004141 0.40282 3.52113
54 3AQV TAK 0.001391 0.40449 3.62319
55 5COU ATP 0.0000008626 0.62103 3.77358
56 2CFM AMP 0.000001289 0.55808 3.77358
57 2Q7D ANP 0.00005501 0.40464 3.77358
58 5LPZ ADP 0.001553 0.40152 3.77358
59 4R78 AMP 0.006495 0.40677 3.8835
60 5A6N U7E 0.009869 0.4212 3.88693
61 2VN9 GVD 0.003718 0.41782 3.98671
62 5LPB ADP 0.001708 0.42628 4.05405
63 2YW2 ATP 0.0006161 0.40236 4.08805
64 5HVJ ANP 0.00038 0.48013 4.12698
65 5L8L ADP 0.004683 0.40702 4.2735
66 4IX4 ADP 0.000203 0.50919 4.28571
67 3GC0 AMP 0.0008197 0.43186 4.40252
68 3CY2 MB9 0.0003727 0.40044 4.4586
69 5C1P ADP 0.0004014 0.44417 4.57516
70 1CKN GTP 0.00001172 0.53198 4.71698
71 1CKM GTP 0.000005119 0.46577 4.71698
72 4F9C 0SX 0.0008941 0.40926 4.71698
73 4RDL FUC GAL NDG FUC 0.005258 0.42276 4.87013
74 4L3L 5FI 0.00664 0.44431 4.93421
75 2XOC ADP 0.001624 0.44645 4.98084
76 3GGF GVD 0.002947 0.40354 4.98339
77 3DLS ADP 0.000008115 0.5691 5.03145
78 1BYG STU 0.001992 0.40757 5.03597
79 4AU8 Z3R 0.002602 0.41792 5.06757
80 1UNH IXM 0.0007903 0.46732 5.13699
81 3O0G 3O0 0.002731 0.44534 5.13699
82 2WQN ADP 0.0005932 0.43303 5.16129
83 3FW3 GLC 0.01514 0.41323 5.26316
84 4IZY 1J2 0.00006973 0.42572 5.34591
85 3UIM ANP 0.0008694 0.40489 5.34591
86 1XDN ATP 0.00000002837 0.58631 5.41516
87 5AWM ANP 0.0005508 0.44396 5.66038
88 5DBX ANP 0.004003 0.40269 5.66038
89 5CEO 50D 0.003611 0.44139 5.66667
90 3HAV ATP 0.00009852 0.50731 5.68562
91 3PLS ANP 0.0006602 0.41933 5.7047
92 1V0O INR 0.0009322 0.40424 5.90278
93 4IDT T28 0.0021 0.4003 5.97484
94 1K3A ACP 0.002364 0.44373 6.02007
95 5LVP ATP 0.001403 0.42053 6.10932
96 3DAK ANP 0.001228 0.40185 6.2069
97 4CQB MLI 0.009145 0.4146 6.28931
98 2QX0 PH2 0.008186 0.41104 6.28931
99 5TT6 ATP 0.00002949 0.4283 6.60377
100 3I0O ADP 0.004734 0.40299 6.60377
101 4DFU QUE 0.001399 0.44646 6.91824
102 3HZT J60 0.001319 0.43075 6.91824
103 4IJP 1EH 0.02604 0.40134 6.91824
104 4PZ6 GMP 0.00001691 0.5431 7.2327
105 4ME6 ADP 0.007193 0.41316 7.77202
106 5HES 032 0.001255 0.47078 7.81759
107 4M69 ANP 0.004372 0.44112 8.12721
108 3VSV XYS 0.007526 0.41834 8.1761
109 2HGS ADP 0.0003652 0.40376 8.1761
110 5XG5 A2G 0.01557 0.40339 8.27586
111 2F2U M77 0.002291 0.41923 8.49057
112 3TII ANP 0.00496 0.40599 8.49057
113 3V8S 0HD 0.001781 0.40161 8.80503
114 3TXO 07U 0.003619 0.40216 9.1195
115 4Y8D 49J 0.002749 0.43224 9.28571
116 4NAT 2W5 0.04949 0.40605 10
117 2IF8 ADP 0.008182 0.40925 10.3774
118 1ZY5 ANP 0.001523 0.40504 10.8911
119 3H9R TAK 0.008464 0.40213 11.0092
120 4C2W ANP 0.002409 0.41821 11.5385
121 1W2D ADP 0.006136 0.40039 13.5849
122 1M0W ANP 0.008768 0.41772 14.1509
123 2A19 ANP 0.000261 0.45932 15.1408
124 3ZRM ZRM 0.0001393 0.43714 25
125 4H3P ANP 0.0009966 0.40842 29.1667
126 4DC2 ADE 0.0005463 0.46842 35.7143
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