Receptor
PDB id Resolution Class Description Source Keywords
3E2M 2 Å NON-ENZYME: IMMUNE LFA-1 I DOMAIN BOUND TO INHIBITORS HOMO SAPIENS INTEGRIN I-DOMAIN LEUKOCYTE FUNCTION ASSOCIATED ANTIGEN-1 ALTERNATIVE SPLICING CALCIUM CELL ADHESION GLYCOPROTEINMAGNESIUM MEMBRANE POLYMORPHISM RECEPTOR TRANSMEMBRANE
Ref.: STRUCTURE-ACTIVITY RELATIONSHIP OF ORTHO- AND META-PHENOL BASED LFA-1 ICAM INHIBITORS BIOORG.MED.CHEM.LETT. V. 18 5245 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
E2M A:1;
B:1;
Valid;
Valid;
none;
none;
ic50 = 0.4 nM
617.6 C29 H29 F6 N O5 S c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3E2M 2 Å NON-ENZYME: IMMUNE LFA-1 I DOMAIN BOUND TO INHIBITORS HOMO SAPIENS INTEGRIN I-DOMAIN LEUKOCYTE FUNCTION ASSOCIATED ANTIGEN-1 ALTERNATIVE SPLICING CALCIUM CELL ADHESION GLYCOPROTEINMAGNESIUM MEMBRANE POLYMORPHISM RECEPTOR TRANSMEMBRANE
Ref.: STRUCTURE-ACTIVITY RELATIONSHIP OF ORTHO- AND META-PHENOL BASED LFA-1 ICAM INHIBITORS BIOORG.MED.CHEM.LETT. V. 18 5245 2008
Members (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 199 families.
1 1XDD ic50 = 0.2 uM AAY C37 H49 N O6 CC[C@H](C)....
2 3F78 - ICF C3 H2 Cl F5 O [C@H](C(F)....
3 1XUO ic50 = 69 nM LA1 C33 H36 N4 O3 CC(C)C[C@H....
4 3M6F - BJZ C26 H19 Cl2 N5 O4 CN1C(=O)N(....
5 1RD4 Kd = 18.3 nM L08 C25 H26 N4 O4 S CCOc1ccccc....
6 1XDG ic50 = 0.05 uM AB8 C34 H48 N2 O7 CC[C@H](C)....
7 2O7N ic50 = 15 nM 2O7 C22 H15 Cl2 N3 O c1cc(ccc1C....
8 3E2M ic50 = 0.4 nM E2M C29 H29 F6 N O5 S c1ccc(c(c1....
9 3BQM Ki = 2 nM BQM C21 H18 F6 N2 O2 S c1cc(cc(c1....
10 2ICA ic50 = 20 nM 2IC C26 H20 Cl2 N4 O4 S CN1C(=O)N(....
11 3BQN ic50 = 2.5 nM BQN C27 H22 F6 N2 O3 S c1ccc(c(c1....
70% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 65 families.
1 1XDD ic50 = 0.2 uM AAY C37 H49 N O6 CC[C@H](C)....
2 3F78 - ICF C3 H2 Cl F5 O [C@H](C(F)....
3 1XUO ic50 = 69 nM LA1 C33 H36 N4 O3 CC(C)C[C@H....
4 3M6F - BJZ C26 H19 Cl2 N5 O4 CN1C(=O)N(....
5 1RD4 Kd = 18.3 nM L08 C25 H26 N4 O4 S CCOc1ccccc....
6 1XDG ic50 = 0.05 uM AB8 C34 H48 N2 O7 CC[C@H](C)....
7 2O7N ic50 = 15 nM 2O7 C22 H15 Cl2 N3 O c1cc(ccc1C....
8 3E2M ic50 = 0.4 nM E2M C29 H29 F6 N O5 S c1ccc(c(c1....
9 3BQM Ki = 2 nM BQM C21 H18 F6 N2 O2 S c1cc(cc(c1....
10 2ICA ic50 = 20 nM 2IC C26 H20 Cl2 N4 O4 S CN1C(=O)N(....
11 3BQN ic50 = 2.5 nM BQN C27 H22 F6 N2 O3 S c1ccc(c(c1....
50% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 43 families.
1 1XDD ic50 = 0.2 uM AAY C37 H49 N O6 CC[C@H](C)....
2 3F78 - ICF C3 H2 Cl F5 O [C@H](C(F)....
3 1XUO ic50 = 69 nM LA1 C33 H36 N4 O3 CC(C)C[C@H....
4 3M6F - BJZ C26 H19 Cl2 N5 O4 CN1C(=O)N(....
5 1RD4 Kd = 18.3 nM L08 C25 H26 N4 O4 S CCOc1ccccc....
6 1XDG ic50 = 0.05 uM AB8 C34 H48 N2 O7 CC[C@H](C)....
7 2O7N ic50 = 15 nM 2O7 C22 H15 Cl2 N3 O c1cc(ccc1C....
8 3E2M ic50 = 0.4 nM E2M C29 H29 F6 N O5 S c1ccc(c(c1....
9 3BQM Ki = 2 nM BQM C21 H18 F6 N2 O2 S c1cc(cc(c1....
10 2ICA ic50 = 20 nM 2IC C26 H20 Cl2 N4 O4 S CN1C(=O)N(....
11 3BQN ic50 = 2.5 nM BQN C27 H22 F6 N2 O3 S c1ccc(c(c1....
12 4XW2 - SIM C25 H40 O6 CCC(C)(C)C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: E2M; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 E2M 1 1
2 BQN 0.669903 0.878788
3 BQM 0.514563 0.764706
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3E2M; Ligand: E2M; Similar sites found: 87
This union binding pocket(no: 1) in the query (biounit: 3e2m.bio3) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1ULE GLA GAL NAG 0.002138 0.45867 None
2 5FPX GLY SER SER HIS HIS HIS HIS HIS 0.0007053 0.45278 None
3 3RF4 FUN 0.02055 0.4129 None
4 5HA0 LTD 0.003193 0.40889 None
5 3BRN SRO 0.02966 0.40536 None
6 2HKA C3S 0.01062 0.40068 None
7 3RGA LSB 0.01284 0.40358 1.62162
8 4MPO AMP 0.01982 0.40833 1.96078
9 4BQY FNT 0.008555 0.40165 2.16216
10 1EPB REA 0.002076 0.44016 2.43902
11 3MTX PGT 0.001576 0.42868 2.64901
12 2XK9 XK9 0.001628 0.43202 2.7027
13 4H69 10Y 0.008353 0.41597 2.7027
14 3W68 VIV 0.002886 0.40228 2.7027
15 4J7Q B7N 0.008543 0.40192 2.7027
16 4ITH RCM 0.002301 0.40081 2.7027
17 2G30 ALA ALA PHE 0.0002808 0.46852 3.24324
18 3PUA OGA 0.01839 0.41573 3.24324
19 4C2C ALA ALA ALA 0.0353 0.40699 3.24324
20 1NYW DAU 0.001004 0.40608 3.24324
21 1T27 PCW 0.01012 0.40598 3.24324
22 1KDK DHT 0.004913 0.40569 3.38983
23 2WA4 069 0.0009163 0.4663 3.78378
24 2Y3S TIR 0.0008709 0.44463 3.78378
25 3G5D 1N1 0.007775 0.41622 3.78378
26 5BVE 4VG 0.0209 0.40381 3.78378
27 5NBW 8SK 0.02133 0.40016 3.78378
28 1QY1 PRZ 0.00111 0.41309 4.02299
29 5ML3 DL3 0.009287 0.40259 4.02685
30 4KBA 1QM 0.002631 0.45406 4.32432
31 1OFL NGK GCD 0.006491 0.44177 4.32432
32 3KRR DQX 0.006125 0.42909 4.32432
33 2WSA MYA 0.03028 0.40702 4.32432
34 2WSA 646 0.03028 0.40702 4.32432
35 1IF7 SBR 0.04181 0.40313 4.32432
36 4JH6 FCN 0.0003875 0.49622 4.34783
37 2OVD DAO 0.002316 0.46469 4.3956
38 4MNS 2AX 0.004668 0.42503 4.40252
39 3TL1 JRO 0.02607 0.40746 4.40252
40 4IAW LIZ 0.003099 0.44545 4.86486
41 3ZJX BOG 0.03155 0.40401 4.86486
42 3FW4 CAQ 0.004295 0.40214 5.05618
43 5C5T AKG 0.02992 0.40028 5.40541
44 2GJ5 VD3 0.006151 0.41014 5.55556
45 2VWA PTY 0.03302 0.40406 5.94059
46 5DRB 5FJ 0.008113 0.41195 5.94595
47 2Q8C AKG 0.02118 0.41162 5.94595
48 2G50 PYR 0.01607 0.40719 5.94595
49 3LVW GSH 0.007581 0.40522 5.94595
50 3KA2 2NC 0.01701 0.4021 5.94595
51 2ZHL NAG GAL GAL NAG 0.006674 0.42465 6.08108
52 4BVA T3 0.002726 0.42727 6.48649
53 5IVE 6E8 0.002663 0.41794 6.48649
54 3KV4 OGA 0.03769 0.40113 6.48649
55 1C1L GAL BGC 0.004667 0.44196 6.56934
56 2BYC FMN 0.01436 0.40851 7.29927
57 4FE2 AIR 0.001181 0.46617 7.56757
58 4N14 WR7 0.02812 0.40397 7.56757
59 5GM5 CBI 0.01086 0.40025 7.56757
60 5DQ8 FLF 0.004057 0.41043 8.10811
61 3A6T 8OG 0.00263 0.43542 8.52713
62 2XMY CDK 0.005781 0.43089 8.64865
63 1AUA BOG 0.002161 0.46395 9.72973
64 5EW9 5VC 0.01227 0.43187 9.72973
65 2E5A LAQ 0.003364 0.41097 9.72973
66 1O9U ADZ 0.02472 0.40712 9.72973
67 2HZQ STR 0.01453 0.42217 9.77011
68 3KO0 TFP 0.00272 0.45779 9.90099
69 5E89 TD2 0.01123 0.40628 10.0719
70 5AIG VPR 0.02546 0.40002 10.4
71 3GXO MQA 0.0243 0.40492 10.8108
72 1OUK 084 0.03807 0.4084 11.8919
73 4XCP PLM 0.01765 0.42093 12.9412
74 3AVR OGA 0.01239 0.42585 12.973
75 2AGC DAO 0.008417 0.42842 13.5802
76 3B6R ADP 0.01332 0.40285 14.0541
77 1DZK PRZ 0.0115 0.4058 14.6497
78 3Q8G PEE 0.005221 0.42704 15.1351
79 2A1L PCW 0.00862 0.4099 16.2162
80 3VQ2 LP4 LP5 MYR DAO 0.001875 0.43738 16.6667
81 4OPC PGT 0.00319 0.46226 17.8378
82 4OPC FDA 0.003652 0.45631 17.8378
83 1SDW IYT 0.005337 0.42934 18.3784
84 1MDC PLM 0.001228 0.41569 20.4545
85 3ZGJ RMN 0.02822 0.40565 21.0811
86 2IYG FMN 0.01622 0.40594 21.7742
87 4ZU4 4TG 0.0009572 0.40598 22.973
Pocket No.: 2; Query (leader) PDB : 3E2M; Ligand: E2M; 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: 3e2m.bio1) has 52 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3E2M; Ligand: E2M; Similar sites found: 33
This union binding pocket(no: 3) in the query (biounit: 3e2m.bio1) has 55 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2NPA MMB 0.008058 0.42799 None
2 4F4S EFO 0.04189 0.42191 None
3 1LFO OLA 0.01506 0.42113 None
4 4LWU 20U 0.02599 0.41876 None
5 3P7N FMN 0.02615 0.40945 None
6 1K7L 544 0.01526 0.40475 None
7 2GC0 PAN 0.04189 0.40212 None
8 4YGF AZM 0.01329 0.42377 1.08108
9 1TT8 PHB 0.01921 0.40038 1.82927
10 3OGN 3OG 0.03337 0.40707 2.41935
11 3W54 RNB 0.03042 0.40908 2.7027
12 1XVB 3BR 0.04396 0.41335 2.94118
13 5LOF 70R 0.009696 0.4062 3.24324
14 3FW3 ETS 0.03603 0.40263 3.24324
15 2CM4 RCL 0.02431 0.40554 3.33333
16 5F2T PLM 0.03101 0.41164 3.78378
17 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.02149 0.43703 4.08163
18 3IX9 MTX 0.02625 0.42194 4.32432
19 5MOB A8S 0.03559 0.41836 4.32432
20 5C3R AKG 0.01889 0.41938 4.86486
21 5C3R HMU 0.01889 0.41938 4.86486
22 3T4L ZEA 0.02791 0.41095 4.86486
23 4TXE 38F 0.02294 0.4183 5.40541
24 4Q5H ANP 0.02271 0.41541 7.05128
25 1N9L FMN 0.02194 0.41317 7.33945
26 3TDC 0EU 0.0005761 0.52938 7.56757
27 1UNB AKG 0.01539 0.40002 8.10811
28 3AJH BL3 0.02385 0.41744 9.18919
29 3KV5 OGA 0.03764 0.43069 12.4324
30 3PUR 2HG 0.02411 0.43808 14.0541
31 5AHS COA 0.01135 0.43736 14.5946
32 3ALN ANP 0.02147 0.41976 21.6216
33 4OAS 2SW 0.01976 0.42493 21.875
Pocket No.: 4; Query (leader) PDB : 3E2M; Ligand: E2M; Similar sites found: 18
This union binding pocket(no: 4) in the query (biounit: 3e2m.bio2) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1Y9Q MED 0.02647 0.41005 2.16216
2 4ZOM 4Q3 0.02218 0.4047 2.16216
3 5L9B AKG 0.03355 0.40039 2.16216
4 1NF8 BOG 0.03743 0.40869 2.7027
5 4H6B 10Y 0.02105 0.40692 3.24324
6 3OPT AKG 0.03769 0.40142 3.78378
7 2PR5 FMN 0.01148 0.40207 3.78788
8 4YV5 SVR 0.04352 0.40631 4.09836
9 3B9Z CO2 0.0245 0.44325 4.32432
10 1OLM VTQ 0.002999 0.40575 4.32432
11 1I7A PHE 0.0188 0.40716 4.5045
12 5MRH Q9Z 0.03385 0.4002 4.86486
13 5U9J GER 0.02121 0.41071 5.32544
14 3B6C SDN 0.03568 0.40293 7.02703
15 2VO4 4NM 0.04834 0.41336 7.56757
16 5HCY 60D 0.006832 0.40806 7.56757
17 3QSB 743 0.02369 0.40433 7.56757
18 1A5Z FBP 0.03012 0.4064 10.2703
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