Receptor
PDB id Resolution Class Description Source Keywords
4GLW 2 Å EC: 6.5.1.2 DNA LIGASE A IN COMPLEX WITH INHIBITOR STREPTOCOCCUS PNEUMONIAE DNA LIGASE A INHIBITOR LIGASE-LIGASE INHIBITOR COMPLEX
Ref.: STRUCTURE-GUIDED DESIGN, SYNTHESIS AND BIOLOGICAL E OF NOVEL DNA LIGASE INHIBITORS WITH IN VITRO AND IN ANTI-STAPHYLOCOCCAL ACTIVITY. BIOORG.MED.CHEM.LETT. V. 22 6705 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
0XT A:402;
B:402;
Valid;
Valid;
none;
none;
Kd = 0.8 uM
206.205 C8 H10 N6 O Cc1c(...
NMN B:403;
Valid;
none;
submit data
335.227 C11 H16 N2 O8 P c1cc(...
SO4 A:401;
B:401;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4GLW 2 Å EC: 6.5.1.2 DNA LIGASE A IN COMPLEX WITH INHIBITOR STREPTOCOCCUS PNEUMONIAE DNA LIGASE A INHIBITOR LIGASE-LIGASE INHIBITOR COMPLEX
Ref.: STRUCTURE-GUIDED DESIGN, SYNTHESIS AND BIOLOGICAL E OF NOVEL DNA LIGASE INHIBITORS WITH IN VITRO AND IN ANTI-STAPHYLOCOCCAL ACTIVITY. BIOORG.MED.CHEM.LETT. V. 22 6705 2012
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 4GLW Kd = 0.8 uM 0XT C8 H10 N6 O Cc1c(nc2c(....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 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(....
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: 0XT; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 0XT 1 1
2 DX1 0.42 0.75
Ligand no: 2; Ligand: NMN; Similar ligands found: 19
No: Ligand ECFP6 Tc MDL keys Tc
1 NMN 1 1
2 NNR 0.693548 0.818182
3 NCN 0.647887 0.892308
4 8ID 0.524752 0.807692
5 NGD 0.514563 0.831169
6 NAD 0.509434 0.875
7 NHD 0.509434 0.875
8 NAJ 0.504762 0.875
9 NAD IBO 0.5 0.815789
10 NDO 0.491071 0.888889
11 NAP 0.486726 0.888889
12 NFD 0.486239 0.828947
13 NBP 0.465517 0.831169
14 NAJ PYZ 0.464912 0.797468
15 DND 0.461538 0.851351
16 NXX 0.461538 0.851351
17 A3D 0.421053 0.863014
18 N01 0.417391 0.849315
19 NA0 0.404959 0.876712
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4GLW; Ligand: NMN; Similar sites found: 65
This union binding pocket(no: 1) in the query (biounit: 4glw.bio1) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3LKJ LKJ 0.02909 0.41553 None
2 3UDG TMP 0.006128 0.4109 1.66113
3 4LZB URA 0.005501 0.4092 1.68067
4 3OV6 MK0 0.02425 0.40867 1.96721
5 2BJK NAD 0.03638 0.40582 2.29508
6 5FA6 FAD 0.0463 0.41588 2.62295
7 5FA6 FMN 0.0463 0.41588 2.62295
8 5FA6 NAP 0.0471 0.41588 2.62295
9 4UCI ADN 0.005183 0.40536 2.62295
10 4HWT 1B2 0.006029 0.4369 2.95082
11 1U7Z PMT 0.0396 0.41002 3.09735
12 2Q89 6CS 0.01363 0.42062 3.11284
13 5FL5 82E 0.01859 0.41028 3.11284
14 1O5O U5P 0.01021 0.40794 3.16742
15 3R4S SIA 0.001107 0.44237 3.27869
16 2JK0 ASP 0.01462 0.4016 3.27869
17 2X4Z X4Z 0.01966 0.4228 3.37838
18 4Q0L V14 0.03304 0.41047 3.80228
19 2QIA U20 0.02724 0.40833 3.81679
20 2WR8 SAH 0.01001 0.41583 3.861
21 3E9I XAH 0.04641 0.40902 3.93443
22 1I36 NAP 0.007348 0.4188 4.16667
23 2HIM ASP 0.00574 0.41689 4.2623
24 1G51 AMP 0.007608 0.40561 4.2623
25 5GXU FMN 0.02477 0.40231 4.2623
26 1WF3 GNP 0.01311 0.41926 4.31894
27 2IMP NAI 0.01518 0.43683 4.59016
28 4R84 CSF 0.007721 0.42637 4.59016
29 2XIQ MLC 0.03934 0.41151 4.59016
30 5W8V 9YP 0.03029 0.40455 4.65116
31 2FP2 TSA 0.02406 0.40232 4.81928
32 4G9N NGA 0.003116 0.405 4.8951
33 5C5H 4YB 0.02365 0.41434 4.91803
34 1JIF CU BLM 0.0111 0.4091 4.91803
35 1ATL 0QI 0.04564 0.40283 4.9505
36 4OWK NGA 0.006562 0.40541 5.07246
37 1UWZ THU 0.03171 0.4116 5.14706
38 4AF0 IMP 0.01664 0.41119 5.2459
39 2PN6 GLN 0.02919 0.40427 5.33333
40 5FLJ QUE 0.02267 0.40419 5.37634
41 4B0T ADP 0.01101 0.42639 5.57377
42 4ER2 IVA VAL VAL STA ALA STA 0.04385 0.41797 5.57377
43 3AJ6 NGA 0.002763 0.40433 5.59441
44 4C0R GDS 0.007814 0.41068 5.64516
45 1QPR PPC 0.01682 0.40478 5.98592
46 3IQE F42 0.03771 0.41174 6.00707
47 5L2J 70E 0.04257 0.42958 6.12245
48 5L2J 6UL 0.04092 0.42958 6.12245
49 3UKR CKH 0.001702 0.46423 6.22951
50 1DL5 SAH 0.02835 0.40546 6.55738
51 2W9S NDP 0.01479 0.40425 6.8323
52 3ZQ6 ADP ALF 0.03926 0.4156 6.88525
53 2PTZ PAH 0.01384 0.40795 7.21311
54 3DZ6 M8E 0.01509 0.40967 7.46269
55 1RYA GDP 0.01934 0.41211 7.5
56 4CO3 ATP 0.02393 0.40127 8.03571
57 1FDQ HXA 0.006881 0.45871 8.39695
58 5XDT MB3 0.04542 0.41061 9.18033
59 4DSU BZI 0.01002 0.40607 9.52381
60 4NG2 OHN 0.01318 0.41121 9.73451
61 1APZ ASP 0.002894 0.40928 9.87654
62 3ZW2 GLA NAG GAL FUC 0.02775 0.40941 10.3448
63 3ZW2 NAG GAL FUC 0.02142 0.40614 10.3448
64 2Q97 ATP 0.00788 0.40832 10.4918
65 2QZ3 XYP XYP XYP 0.02444 0.40499 12.4324
Pocket No.: 2; Query (leader) PDB : 4GLW; Ligand: 0XT; 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: 4glw.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4GLW; Ligand: 0XT; Similar sites found: 158
This union binding pocket(no: 3) in the query (biounit: 4glw.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2CSN CKI 0.00374 0.44789 1.3468
2 3AKK ADP 0.002428 0.4467 1.63934
3 1RE8 BD2 0.01151 0.44194 1.63934
4 4JR7 GNP 0.0008168 0.41362 1.63934
5 4AZT LY2 0.006329 0.40489 1.63934
6 1NZY BCA 0.01665 0.41747 1.85874
7 3DLS ADP 0.00009433 0.5086 1.96721
8 4UAL 3FV 0.007105 0.42165 1.96721
9 5GZ9 ANP 0.01102 0.41934 1.96721
10 5DBX ANP 0.009957 0.40804 1.96721
11 5JKG 6LF 0.04851 0.40186 1.96721
12 2QCS ANP 0.007889 0.43135 2.06186
13 3VPC ADP 0.000385 0.40478 2.12766
14 2R7K AMZ 0.0005318 0.49434 2.29508
15 1IOW PHY 0.001705 0.47531 2.29508
16 2PZI AXX 0.0004585 0.44556 2.29508
17 3X01 AMP 0.00273 0.43732 2.29508
18 4BTK DTQ 0.003597 0.43621 2.29508
19 1I7L ATP 0.00002228 0.4336 2.29508
20 4KBA 1QM 0.007671 0.40854 2.29508
21 1BYG STU 0.01263 0.40524 2.51799
22 2OFV 242 0.01688 0.42427 2.52708
23 4H6B 10X 0.00435 0.4067 2.5641
24 2VPQ ANP 0.001842 0.45844 2.62295
25 4IX4 ADP 0.002653 0.44678 2.62295
26 4PZ6 GMP 0.0006709 0.43071 2.62295
27 4EUU BX7 0.009487 0.42726 2.62295
28 4U98 ACP 0.00133 0.41128 2.62295
29 3Q60 ATP 0.01172 0.40893 2.62295
30 4CYI ATP 0.01958 0.40171 2.62295
31 2J4D FAD 0.03467 0.40092 2.62295
32 4USF 6UI 0.008901 0.42563 2.63158
33 2J7T 274 0.007623 0.43631 2.64901
34 3HAV ATP 0.00002955 0.49858 2.67559
35 2ZV2 609 0.002556 0.42287 2.68456
36 4Y0X ADP 0.0004172 0.43839 2.93333
37 5DZT AMP 0.0002136 0.49246 2.95082
38 2V7O DRN 0.0009459 0.45177 2.95082
39 5JFS 6K0 0.01546 0.43041 2.95082
40 2WQN ADP 0.002434 0.41606 2.95082
41 2Q4H AMP 0.01807 0.41429 2.95082
42 4O1P ANP 0.01067 0.41292 2.95082
43 4U0I 0LI 0.02516 0.41063 2.95082
44 3NW7 LGV 0.04356 0.41052 2.95082
45 4K33 ACP 0.01646 0.40548 2.95082
46 2VN9 GVD 0.004685 0.41874 2.99003
47 1K3A ACP 0.003426 0.43045 3.01003
48 1PHK ATP 0.0098 0.41667 3.02013
49 3VPD ANP 0.0007013 0.47754 3.20285
50 3SRV S19 0.006284 0.42221 3.2491
51 3HZT J60 0.0009931 0.44157 3.27869
52 2B9F ADP 0.007002 0.42196 3.27869
53 1OBD ATP 0.002702 0.41605 3.27869
54 1NP7 FAD 0.02686 0.40669 3.27869
55 4F4P 0SB 0.01948 0.43795 3.2967
56 4AU8 Z3R 0.001446 0.43387 3.37838
57 4OCJ NDG 0.007387 0.4454 3.60656
58 3OFM 4B0 0.003317 0.43112 3.60656
59 4DFU QUE 0.006476 0.41204 3.60656
60 1EHI ADP 0.0007671 0.40244 3.60656
61 2F2U M77 0.0052 0.40177 3.60656
62 1XDN ATP 0.0001708 0.45121 3.61011
63 1S68 AMP 0.003041 0.42225 3.61446
64 2XVD AS6 0.01598 0.41839 3.64238
65 4I94 ANP 0.001553 0.45191 3.66667
66 3PLS ANP 0.006205 0.42248 3.69128
67 4IWN GEK 0.02501 0.40283 3.93013
68 2HGS ADP 0.0003618 0.49393 3.93443
69 5TDF ADP 0.000701 0.47552 3.93443
70 5AWM ANP 0.0004886 0.45517 3.93443
71 1CKN GTP 0.001532 0.44183 3.93443
72 3UDZ ADP 0.005083 0.43081 3.93443
73 4AUA 4AU 0.0008678 0.42049 3.93443
74 1CKM GTP 0.0005088 0.40606 3.93443
75 1GSA ADP 0.000115 0.51892 4.2623
76 2CFM AMP 0.0005861 0.45207 4.2623
77 2R85 AMP 0.007561 0.4378 4.2623
78 1M0W ANP 0.004243 0.42833 4.2623
79 2Q7D ANP 0.0001111 0.41117 4.2623
80 4C2V YJA 0.02244 0.41323 4.5614
81 3DNT ATP 0.001363 0.46681 4.59016
82 3V8S 0HD 0.002438 0.44233 4.59016
83 3ZRM ZRM 0.00351 0.43673 4.59016
84 1O9U ADZ 0.001886 0.43027 4.59016
85 4U44 3D9 0.005651 0.42655 4.59016
86 3F7Z 34O 0.01007 0.41417 4.59016
87 1ZY5 ANP 0.00344 0.43502 4.62046
88 3M2W L8I 0.00825 0.412 4.68227
89 5A5W GUO 0.01702 0.42915 4.74308
90 5COU ATP 0.0002789 0.48835 4.91803
91 3E7O 35F 0.005316 0.44573 4.91803
92 5FI4 5XV 0.005644 0.43564 4.91803
93 2B9H ADP 0.01257 0.4113 4.91803
94 1ME8 RVP 0.03789 0.40763 4.91803
95 3BU5 ATP 0.01419 0.40681 4.91803
96 4L3L 5FI 0.006313 0.44054 4.93421
97 3CQL NAG 0.01494 0.40269 4.93827
98 1IA9 ANP 0.00005604 0.44731 5
99 4OAV ACP 0.01154 0.40926 5.2459
100 2BKK ADP 0.003273 0.43141 5.32544
101 1E4E ADP 0.0006088 0.47641 5.57377
102 3VOT ADP 0.0003796 0.47366 5.57377
103 3WVR AMP 0.001458 0.45088 5.57377
104 1Q8Y ADE 0.001452 0.44293 5.57377
105 4XH0 ADP 0.002759 0.43712 5.57377
106 1Q8Y ADP 0.0135 0.41155 5.57377
107 3OJF NDP 0.04581 0.40223 5.83658
108 5LXC 7AA 0.002168 0.44251 5.90164
109 4UWH JXM 0.0006486 0.43242 5.90164
110 4YZC STU 0.02215 0.41909 5.90164
111 4XYM A12 0.0004093 0.41613 5.90164
112 4YMJ 4EJ 0.001514 0.45077 5.92105
113 5IQD GNP 0.008584 0.44086 6.22951
114 5IQD RIO 0.008999 0.44086 6.22951
115 5NBW 8SK 0.001307 0.4269 6.30631
116 1MEX RAC 0.007822 0.41071 6.51163
117 5C4L 4XR 0.001614 0.47251 6.55738
118 5C4L SIS 0.01136 0.42863 6.55738
119 2XK9 XK9 0.04092 0.40386 6.55738
120 3O0G 3O0 0.00404 0.4316 6.71141
121 3HSS MLA 0.00451 0.41646 6.82594
122 3TKI S25 0.03305 0.42172 6.88525
123 4ZS4 ATP 0.0009748 0.40543 6.88525
124 1H2T GDP 7MG 0.01723 0.40069 7.05128
125 3TY5 ADP 0.000877 0.42837 7.21311
126 4YLL 4E3 0.01548 0.41188 7.47922
127 2J9D ADP 0.01648 0.4105 7.56302
128 2QK4 ATP 0.003312 0.4259 7.86885
129 4DC2 ADE 0.002458 0.40816 7.86885
130 3FWN ATR 0.03818 0.40547 7.86885
131 1O5R FR9 0.04112 0.40055 7.86885
132 2A19 ANP 0.005266 0.41012 8
133 1UNH IXM 0.005071 0.42222 8.17308
134 4ME6 ADP 0.001924 0.4447 8.19672
135 4H3P ANP 0.00822 0.41852 8.19672
136 4H3Q ANP 0.01205 0.41738 8.19672
137 5A3T MMK 0.03077 0.40604 8.19672
138 1U59 STU 0.001294 0.40698 8.36237
139 4CFU 2WC 0.00456 0.40019 8.58086
140 4BCM T7Z 0.007877 0.40351 8.63787
141 4BCN T9N 0.003587 0.4105 8.66667
142 4G17 0VN 0.007034 0.41764 8.85246
143 5UIU 8CG 0.01373 0.42309 9.18033
144 5HVJ ANP 0.01069 0.4081 9.18033
145 5MW8 ATP 0.005854 0.43319 9.5082
146 4HIA FMN 0.03717 0.40609 10.2273
147 1AUX AGS 0.0002015 0.43941 10.4918
148 1PK8 ATP 0.00009049 0.41205 10.4918
149 2YAK OSV 0.01721 0.418 10.5263
150 1MJJ HAL 0.01733 0.41095 11.4155
151 2TPS TPS 0.02478 0.40588 11.4537
152 3ETH ATP 0.0006424 0.47945 11.8033
153 4NST ADP 0.001625 0.45319 12.3134
154 2GAG FAD 0.04039 0.41391 13.1313
155 2GAG FOA 0.04039 0.41391 13.1313
156 5C1P ADP 0.001044 0.42927 13.7705
157 5K2M ADP 0.0004891 0.48926 16.9811
158 4WW7 AMP 0.003391 0.44334 17.1123
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