Receptor
PDB id Resolution Class Description Source Keywords
2DM6 2 Å EC: 1.3.1.48 CRYSTAL STRUCTURE OF ANTI-CONFIGURATION OF INDOMETHACIN AND LEUKOTRIENE B4 12-HYDROXYDEHYDROGENASE/15-OXO- P ROSTAGLANDIN 13-REDUCTASE COMPLEX CAVIA PORCELLUS NAD(P)-BINDING ROSSMANN-FOLD DOMAINS RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI STRUCTURAL GENOMICS OXIDOREDUCTASE
Ref.: CRYSTAL STRUCTURE OF ANTI-CONFIGURATION OF INDOMETHACIN AND LEUKOTRIENE B4 12-HYDROXYDEHYDROGENASE/15-OXO-PROSTAGLANDIN 13-REDUCTASE COMPLEX REVEALS THE STRUCTURAL BASIS OF BROAD SPECTRUM INDOMETHACIN EFFICACY J.BIOCHEM.(TOKYO) V. 140 4
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
IMN A:1401;
Valid;
none;
ic50 = 97.9 uM
357.788 C19 H16 Cl N O4 Cc1c(...
NAP A:1400;
B:2400;
Valid;
Valid;
none;
none;
submit data
743.405 C21 H28 N7 O17 P3 c1cc(...
TAM B:5000;
Invalid;
none;
submit data
163.215 C7 H17 N O3 C(CO)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2DM6 2 Å EC: 1.3.1.48 CRYSTAL STRUCTURE OF ANTI-CONFIGURATION OF INDOMETHACIN AND LEUKOTRIENE B4 12-HYDROXYDEHYDROGENASE/15-OXO- P ROSTAGLANDIN 13-REDUCTASE COMPLEX CAVIA PORCELLUS NAD(P)-BINDING ROSSMANN-FOLD DOMAINS RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI STRUCTURAL GENOMICS OXIDOREDUCTASE
Ref.: CRYSTAL STRUCTURE OF ANTI-CONFIGURATION OF INDOMETHACIN AND LEUKOTRIENE B4 12-HYDROXYDEHYDROGENASE/15-OXO-PROSTAGLANDIN 13-REDUCTASE COMPLEX REVEALS THE STRUCTURAL BASIS OF BROAD SPECTRUM INDOMETHACIN EFFICACY J.BIOCHEM.(TOKYO) V. 140 4
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1V3V - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
2 1V3T - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
3 2DM6 ic50 = 97.9 uM IMN C19 H16 Cl N O4 Cc1c(c2cc(....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1V3V - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
2 1V3T - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
3 2DM6 ic50 = 97.9 uM IMN C19 H16 Cl N O4 Cc1c(c2cc(....
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2ZB7 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 2ZB8 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
3 2ZB4 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
4 2ZB3 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
5 4B7X - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
6 1V3V - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
7 1V3T - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
8 2DM6 ic50 = 97.9 uM IMN C19 H16 Cl N O4 Cc1c(c2cc(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: IMN; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 IMN 1 1
2 511 0.5 0.92
3 241 0.444444 0.851852
4 240 0.401961 0.851852
Ligand no: 2; Ligand: NAP; Similar ligands found: 127
No: Ligand ECFP6 Tc MDL keys Tc
1 NAP 1 1
2 NA0 0.881356 0.986301
3 TAP 0.872881 0.934211
4 NDO 0.840336 0.972603
5 NAD 0.811966 0.986111
6 N01 0.733871 0.958904
7 A3D 0.712 0.972603
8 NBP 0.707692 0.935065
9 NAD IBO 0.688 0.921053
10 NHD 0.68254 0.958904
11 NJP 0.661417 0.972973
12 NAJ PYZ 0.659091 0.898734
13 NFD 0.658915 0.934211
14 DND 0.619048 0.959459
15 NXX 0.619048 0.959459
16 ZID 0.605839 0.972603
17 NAQ 0.59854 0.922078
18 ATR 0.59292 0.917808
19 NAE 0.591241 0.946667
20 NDE 0.58042 0.986301
21 A22 0.571429 0.958904
22 AMP NAD 0.571429 0.933333
23 NAJ 0.567164 0.986111
24 A2R 0.563025 0.932432
25 NDC 0.561644 0.922078
26 NA7 0.552846 0.907895
27 ODP 0.551471 0.935065
28 A2P 0.539823 0.930556
29 8ID 0.537313 0.910256
30 NAD BBN 0.525974 0.865854
31 NPW 0.525547 0.8875
32 CNA 0.521739 0.959459
33 NZQ 0.521739 0.910256
34 NAD CJ3 0.519231 0.835294
35 NDP 0.514493 0.922078
36 PO4 PO4 A A A A PO4 0.503937 0.930556
37 DG1 0.503401 0.922078
38 1DG 0.503401 0.922078
39 NAD TDB 0.5 0.696078
40 TXP 0.5 0.922078
41 NMN AMP PO4 0.492958 0.921053
42 XNP 0.492958 0.875
43 25L 0.492308 0.958904
44 25A 0.492063 0.972222
45 NAD NDT 0.490909 0.747368
46 NMN 0.486726 0.888889
47 NGD 0.485714 0.935065
48 2AM 0.477876 0.891892
49 ADP 0.458333 0.945205
50 PAP 0.451613 0.931507
51 ADP MG 0.45082 0.906667
52 BEF ADP 0.447154 0.883117
53 ADP BEF 0.447154 0.883117
54 A2D 0.445378 0.945205
55 AN2 0.442623 0.932432
56 ADP PO3 0.44 0.944444
57 SAP 0.44 0.896104
58 AGS 0.44 0.896104
59 M33 0.439024 0.906667
60 AR6 AR6 0.438849 0.945205
61 BA3 0.438017 0.945205
62 ATP MG 0.436508 0.906667
63 ADP BMA 0.43609 0.92
64 OAD 0.43609 0.92
65 ATP 0.435484 0.945205
66 OOB 0.435115 0.958904
67 B4P 0.434426 0.945205
68 AP5 0.434426 0.945205
69 GAP 0.433071 0.92
70 0WD 0.432432 0.922078
71 5FA 0.432 0.945205
72 2A5 0.432 0.87013
73 AQP 0.432 0.945205
74 00A 0.428571 0.909091
75 CA0 0.427419 0.92
76 ALF ADP 0.426357 0.871795
77 ADP ALF 0.426357 0.871795
78 ACP 0.424 0.92
79 NAJ PZO 0.423841 0.897436
80 9SN 0.423358 0.897436
81 VO4 ADP 0.423077 0.932432
82 ANP MG 0.423077 0.896104
83 ADP VO4 0.423077 0.932432
84 WAQ 0.422222 0.884615
85 ACQ 0.421875 0.92
86 V3L 0.421875 0.945205
87 ADQ 0.421053 0.92
88 AR6 0.420635 0.918919
89 APR 0.420635 0.918919
90 ATP A A A 0.42029 0.958333
91 CO7 0.419753 0.786517
92 1ZZ 0.419118 0.841463
93 3OD 0.419118 0.92
94 DLL 0.41791 0.958904
95 AD9 0.417323 0.92
96 NAX 0.416667 0.875
97 OVE 0.416667 0.857143
98 MYR AMP 0.416058 0.841463
99 AV2 0.415385 0.868421
100 A3P 0.414634 0.944444
101 NNR 0.414414 0.72973
102 ALF ADP 3PG 0.413793 0.8625
103 OMR 0.413793 0.831325
104 LA8 ALF 3PG 0.413793 0.8625
105 ANP 0.410853 0.92
106 A1R 0.410448 0.860759
107 ABM 0.409836 0.893333
108 AMP 0.408333 0.944444
109 A 0.408333 0.944444
110 SON 0.408 0.933333
111 PPS 0.407692 0.829268
112 5AL 0.407692 0.932432
113 TYR AMP 0.407143 0.933333
114 NAI 0.406897 0.909091
115 7D3 0.406504 0.857143
116 DAL AMP 0.406015 0.932432
117 ADX 0.404762 0.829268
118 ATF 0.40458 0.907895
119 3UK 0.404412 0.945946
120 AMP DBH 0.404255 0.894737
121 139 0.402685 0.875
122 AMP MG 0.401639 0.893333
123 50T 0.401575 0.906667
124 SRP 0.401515 0.907895
125 A A 0.40146 0.972222
126 FA5 0.4 0.933333
127 3AM 0.4 0.90411
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2DM6; Ligand: IMN; Similar sites found: 114
This union binding pocket(no: 1) in the query (biounit: 2dm6.bio1) has 40 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2DBZ NAP 0.00004877 0.42497 1.2012
2 1CER NAD 0.001753 0.4304 1.20846
3 4E5N NAD 0.0001789 0.41355 1.51515
4 3NJ4 AFX 0.01327 0.40771 1.8018
5 3NJ4 NAD 0.02031 0.40031 1.8018
6 4TUZ 36J 0.01224 0.42123 1.96078
7 3BAZ NAP 0.00001757 0.51689 2.1021
8 1X9I G6Q 0.0372 0.40379 2.31788
9 3TWO NDP 0.00000314 0.48337 2.4024
10 4MDH NAD 0.001833 0.42673 2.4024
11 4K28 NAD 0.004819 0.41502 2.60223
12 5VKT NAP 0.000008429 0.51265 2.7027
13 5FJJ MAN 0.0349 0.41031 2.7027
14 2CDC XYP 0.00369 0.40893 2.7027
15 2CDC XYS 0.003869 0.40817 2.7027
16 2CDC NAP 0.003869 0.40817 2.7027
17 4U7W NDP 0.005823 0.40642 2.7027
18 5GZ6 NDP 0.01589 0.4035 2.76074
19 2B5W NAP 0.0002431 0.44079 3.003
20 2I3G NAP 0.0005672 0.43827 3.003
21 1CDO NAD 0.00002925 0.42736 3.3033
22 2GSD NAD 0.0001534 0.42711 3.3033
23 3OND ADN 0.002062 0.4065 3.3033
24 3OND NAD 0.002062 0.4065 3.3033
25 4OOE NDP 0.007762 0.40382 3.3033
26 2PZI AXX 0.0413 0.40144 3.3033
27 4JMO JAF 0.04926 0.40424 3.5
28 5DN9 NAD 0.0002731 0.44455 3.6036
29 1J78 OLA 0.02933 0.41605 3.6036
30 1VKO NAD 0.00381 0.40409 3.6036
31 1GQ2 NAP 0.0003468 0.40007 3.6036
32 1PZG A3D 0.0009376 0.41482 3.62538
33 5LPG 71V 0.03828 0.41019 3.65854
34 2DT5 NAD 0.0001328 0.46925 3.79147
35 4WNP 3RJ 0.03521 0.40177 3.83275
36 4DPL NAP 0.001352 0.42644 3.9039
37 4XFR CIT 0.01996 0.4261 3.9039
38 2GCG NDP 0.0004108 0.4004 3.93939
39 5NE2 DGL 0.0272 0.42275 3.95683
40 4XWM CBI 0.03445 0.41645 4.2042
41 1TB4 PEJ 0.003349 0.41102 4.2042
42 1LDM NAD 0.001351 0.42644 4.25532
43 2HJR APR 0.00124 0.44623 4.26829
44 2BH9 NAP 0.02409 0.40681 4.5045
45 5JE8 NAD 0.006804 0.40875 4.63576
46 1T26 NAI 0.001262 0.40913 4.96894
47 2F1K NAP 0.001948 0.42852 5.01792
48 4J4H NAI 0.0006877 0.42234 5.01931
49 4J4H 1J1 0.0006877 0.42234 5.01931
50 4JK3 NAD 0.0001157 0.40625 5.01931
51 2VHW NAI 0.0003568 0.41725 5.1051
52 5UXH GFB 0.01636 0.40575 5.1051
53 5N18 8HZ 0.02352 0.4317 5.50459
54 3ABI NAD 0.0000432 0.48491 5.70571
55 3X01 AMP 0.03009 0.42214 6.00601
56 2J5V PCA 0.0425 0.42142 6.00601
57 1HKU NAD 0.0003227 0.4477 6.30631
58 2EV9 SKM 0.003393 0.406 6.46388
59 4XYB NDP 0.0001228 0.45447 6.60661
60 4I9B 1KA 0.04156 0.40212 6.60661
61 2NAD NAD 0.0001584 0.42669 6.90691
62 4PLG NAI 0.0009738 0.40534 7.20721
63 1EZ4 NAD 0.001303 0.43569 7.2327
64 2GZ3 NAP 0.001537 0.4119 7.50751
65 1Z82 NDP 0.008297 0.40019 7.50751
66 2QRK AMP 0.001608 0.40008 7.50751
67 3GFB NAD 0.0000678 0.48457 7.80781
68 4RQU NAD 0.00007311 0.42327 7.80781
69 1NC4 DOF 0.04651 0.40711 7.90698
70 1PL6 572 0.0002124 0.4146 8.10811
71 1R37 NAD 0.000002211 0.4845 8.35735
72 3LXR GDP 0.03606 0.40125 8.64865
73 2YGM GLA NAG GAL FUC 0.03683 0.41109 9.00901
74 4A0S NAP 0.00000004078 0.5977 9.90991
75 1C1X NAD 0.0004856 0.4533 10.2102
76 1BW9 NAD 0.002528 0.43607 10.2102
77 1D1T NAD 0.00001938 0.44725 10.8108
78 5M67 NAD 0.002242 0.40611 11.1111
79 5M67 ADE 0.00248 0.40456 11.1111
80 5M67 3D1 0.002735 0.40306 11.1111
81 1E3I CXF 0.00007596 0.4561 11.4114
82 1ZEM NAD 0.003232 0.41948 12.9771
83 2FZW NAD 0.0004264 0.42652 13.8138
84 3B9Q MLI 0.0276 0.42184 15.5629
85 1LLU NAD 0.000001424 0.4915 16.2162
86 5H81 NAP 0.00007282 0.50395 17.2236
87 2J8Z NAP 0.000000009929 0.53724 17.7177
88 3JYN NDP 0.000000003221 0.57159 17.8462
89 5DOZ NDP 0.000001318 0.53097 18.6186
90 5FI3 NAP 0.0000317 0.49016 19.2192
91 1KOL NAD 0.0005005 0.4133 19.2192
92 3WLE NAD 0.00001842 0.45947 20.1201
93 1U3U BNF 0.000012 0.47905 20.4204
94 1U3U NAD 0.000012 0.46266 20.4204
95 1YQD NAP 0.00003166 0.47946 20.4918
96 4IDC NDP 0.0000005112 0.50115 20.7831
97 4IDC 1XX 0.0000005112 0.50115 20.7831
98 1F8F NAD 0.00001713 0.42698 21.3213
99 3QWB NDP 0.000000000439 0.67342 21.6216
100 4W6Z 8ID 0.00000002829 0.55379 25.5255
101 1P0F NAP 0.000002984 0.47337 25.7373
102 3JV7 NAD 0.00001646 0.50129 25.8258
103 1H2B NAJ 0.000006074 0.46784 26.7267
104 1YKF NAP 0.0002403 0.40677 27.6276
105 4WAS NAP 0.00000007919 0.53894 28.2282
106 4WAS COO 0.0000002026 0.52483 28.2282
107 1N9G NAP 0.0000003979 0.47648 28.2282
108 4GKV NAD 0.00000179 0.48778 28.2738
109 4JBI NDP 0.000002705 0.55083 29.1291
110 1KEV NDP 0.0001068 0.429 29.4294
111 4RVU NDP 0.0000000158 0.59742 30.1205
112 1YB5 NAP 0.00000008061 0.53015 31.2312
113 2DFV NAD 0.0001522 0.40604 36.9369
114 5DP2 NAP 0.000001177 0.47049 43.2432
Pocket No.: 2; Query (leader) PDB : 2DM6; Ligand: NAP; Similar sites found: 103
This union binding pocket(no: 2) in the query (biounit: 2dm6.bio1) has 39 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2DBZ NAP 0.0000838 0.42242 1.2012
2 1CER NAD 0.002039 0.42661 1.20846
3 4BVA T3 0.001517 0.4042 1.5015
4 4E5N NAD 0.0004295 0.4053 1.51515
5 3NJ4 NAD 0.009945 0.41442 1.8018
6 3NJ4 AFX 0.01585 0.40624 1.8018
7 4TUZ 36J 0.01415 0.41717 1.96078
8 3BAZ NAP 0.00004333 0.49918 2.1021
9 3TWO NDP 0.000006382 0.47787 2.4024
10 4MDH NAD 0.0006654 0.44334 2.4024
11 4K28 NAD 0.002701 0.42447 2.60223
12 5VKT NAP 0.00001008 0.50819 2.7027
13 2CDC XYP 0.003116 0.4136 2.7027
14 5FJJ MAN 0.03361 0.4099 2.7027
15 2CDC XYS 0.004407 0.40798 2.7027
16 2CDC NAP 0.004407 0.40798 2.7027
17 5GZ6 NDP 0.01335 0.40594 2.76074
18 2B5W NAP 0.000286 0.43702 3.003
19 2I3G NAP 0.002006 0.41606 3.003
20 1HDG NAD 0.004667 0.41457 3.01205
21 5T7I LAT NAG GAL 0.04585 0.40921 3.22581
22 1CDO NAD 0.00002441 0.43483 3.3033
23 5LD5 NAD 0.005847 0.41603 3.3033
24 3OND NAD 0.001372 0.41487 3.3033
25 3OND ADN 0.001372 0.41487 3.3033
26 2F2U M77 0.02735 0.41333 3.3033
27 2GSD NAD 0.0005534 0.41196 3.3033
28 4OOE NDP 0.006132 0.40701 3.3033
29 5DN9 NAD 0.0005562 0.43185 3.6036
30 5CAD PCA 0.01705 0.42529 3.6036
31 1VKO NAD 0.001237 0.42149 3.6036
32 1GQ2 NAP 0.0003581 0.40242 3.6036
33 1PZG A3D 0.001693 0.40469 3.62538
34 2DT5 NAD 0.0001935 0.46151 3.79147
35 4DPL NAP 0.003273 0.41034 3.9039
36 2GCG NDP 0.000264 0.40657 3.93939
37 1E5Q NDP 0.0001091 0.4189 4.2042
38 4XZ3 COA 0.005317 0.41782 4.2042
39 1LDM NAD 0.004575 0.40467 4.25532
40 2HJR APR 0.006143 0.41511 4.26829
41 1HPG BOC ALA ALA PRO GLU 0.042 0.40016 4.27807
42 2BH9 NAP 0.01429 0.41696 4.5045
43 5JE8 NAD 0.008312 0.4041 4.63576
44 1T26 NAI 0.001764 0.40618 4.96894
45 2F1K NAP 0.001545 0.43154 5.01792
46 4J4H NAI 0.001305 0.41471 5.01931
47 4J4H 1J1 0.001305 0.41471 5.01931
48 4JK3 NAD 0.0002414 0.40078 5.01931
49 2VHW NAI 0.0003793 0.41998 5.1051
50 3ABI NAD 0.0001111 0.4676 5.70571
51 3X01 AMP 0.02367 0.42643 6.00601
52 2WHL MAN BMA BMA 0.04701 0.4036 6.12245
53 1HKU NAD 0.0006113 0.43585 6.30631
54 2EV9 SKM 0.00287 0.40769 6.46388
55 4XYB NDP 0.0002497 0.44192 6.60661
56 2NAD NAD 0.0006323 0.41096 6.90691
57 1EZ4 NAD 0.001511 0.43194 7.2327
58 3GFB NAD 0.00001844 0.50601 7.80781
59 4RQU NAD 0.0001293 0.41724 7.80781
60 1PL6 572 0.0004801 0.40484 8.10811
61 1R37 NAD 0.00000483 0.4788 8.35735
62 4A0S NAP 0.00000008753 0.58321 9.90991
63 1C1X NAD 0.0007604 0.44415 10.2102
64 1BW9 NAD 0.002605 0.43442 10.2102
65 1D1T NAD 0.00001612 0.45347 10.8108
66 5M67 NAD 0.001398 0.41549 11.1111
67 5M67 ADE 0.001496 0.41444 11.1111
68 5M67 3D1 0.001632 0.41308 11.1111
69 5L95 AMP 0.009283 0.41608 11.25
70 1E3I CXF 0.00005466 0.45987 11.4114
71 1ZEM NAD 0.003442 0.41729 12.9771
72 2FZW NAD 0.0003233 0.43313 13.8138
73 3B9Q MLI 0.02606 0.42376 15.5629
74 1LLU NAD 0.000001083 0.50017 16.2162
75 5H81 NAP 0.0003693 0.47169 17.2236
76 2J8Z NAP 0.000000003332 0.55794 17.7177
77 3JYN NDP 0.000000001945 0.58527 17.8462
78 5DOZ NDP 0.000001952 0.52307 18.6186
79 5FI3 NAP 0.0001437 0.46324 19.2192
80 1KOL NAD 0.0006228 0.41318 19.2192
81 3WLE NAD 0.00004284 0.45255 20.1201
82 1U3U BNF 0.0000131 0.48086 20.4204
83 1U3U NAD 0.0000131 0.45872 20.4204
84 1YQD NAP 0.00004204 0.47353 20.4918
85 4IDC 1XX 0.0000009101 0.49791 20.7831
86 4IDC NDP 0.0000009101 0.49791 20.7831
87 1F8F NAD 0.00001433 0.43288 21.3213
88 3QWB NDP 0.0000000002752 0.67913 21.6216
89 4W6Z 8ID 0.00000005597 0.54979 25.5255
90 1P0F NAP 0.000004259 0.47322 25.7373
91 3JV7 NAD 0.00003327 0.48799 25.8258
92 1H2B NAJ 0.000009959 0.46545 26.7267
93 1YKF NAP 0.0002201 0.41042 27.6276
94 4WAS NAP 0.0000001793 0.53273 28.2282
95 4WAS COO 0.000000334 0.52326 28.2282
96 1N9G NAP 0.000000357 0.48211 28.2282
97 4GKV NAD 0.000004139 0.48064 28.2738
98 4JBI NDP 0.000007464 0.53097 29.1291
99 1KEV NDP 0.0001199 0.43095 29.4294
100 4RVU NDP 0.00000000252 0.62476 30.1205
101 1YB5 NAP 0.0000000365 0.54731 31.2312
102 2DFV NAD 0.00005525 0.42318 36.9369
103 5DP2 NAP 0.0000009817 0.47851 43.2432
Pocket No.: 3; Query (leader) PDB : 2DM6; Ligand: NAP; 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: 2dm6.bio1) has 38 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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