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Receptor
PDB id Resolution Class Description Source Keywords
2QHD 1.95 Å EC: 3.1.1.4 CRYSTAL STRUCTURE OF ECARPHOLIN S (SER49-PLA2) COMPLEXED WIT ACID ECHIS CARINATUS BETA SHEET THREE HELICES PROTEIN-LIGAND COMPLEX HYDROLASE
Ref.: STRUCTURAL CHARACTERIZATION OF MYOTOXIC ECARPHOLIN ECHIS CARINATUS VENOM BIOPHYS.J. V. 95 3366 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DAO A:501;
B:502;
Valid;
Valid;
none;
none;
submit data
200.318 C12 H24 O2 CCCCC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2QHD 1.95 Å EC: 3.1.1.4 CRYSTAL STRUCTURE OF ECARPHOLIN S (SER49-PLA2) COMPLEXED WIT ACID ECHIS CARINATUS BETA SHEET THREE HELICES PROTEIN-LIGAND COMPLEX HYDROLASE
Ref.: STRUCTURAL CHARACTERIZATION OF MYOTOXIC ECARPHOLIN ECHIS CARINATUS VENOM BIOPHYS.J. V. 95 3366 2008
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 2QHD - DAO C12 H24 O2 CCCCCCCCCC....
2 3BJW - SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
70% Homology Family (28)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 12 families.
1 2QVD Kd = 0.00000145 M BER C20 H18 N O4 COc1ccc2cc....
2 1ZWP - NIM C13 H12 N2 O5 S CS(=O)(=O)....
3 1OXL - IDA C15 H18 N2 O3 CCCc1cc2cc....
4 1TG4 - PHE LEU ALA TYR LYS n/a n/a
5 1SKG - VAL ALA PHE ARG SER n/a n/a
6 1JQ9 Kd = 3.57 nM PHE LEU SER TYR LYS n/a n/a
7 2ARM Ki = 7.4 nM OIN C17 H23 N O3 CN1[C@H]2C....
8 1FV0 Kd = 1.18 uM 9AR C17 H11 N O8 COc1c(ccc2....
9 1Q7A Kd = 0.064 uM OPB C19 H20 N2 O3 CCCC[C@H]1....
10 1TG1 - PHQ LEU VAL ARG TYR n/a n/a
11 1ZYX - LCF C23 H22 Cl N O2 CC1(Cc2c(c....
12 1TJK - PHE LEU SER THR LYS n/a n/a
13 1KPM Ki = 1.59 uM VIT C29 H50 O2 Cc1c(c2c(c....
14 1TP2 - TDA C13 H26 O2 CCCCCCCCCC....
15 1TDV - TYR TRP ALA ALA ALA ALA n/a n/a
16 1TJ9 - VAL ALA ARG SER n/a n/a
17 1JQ8 Ki = 1.01 uM LEU ALA ILE TYR SER n/a n/a
18 1SQZ - PHQ ILE ALA ARG SER n/a n/a
19 1TGM - AIN C9 H8 O4 CC(=O)Oc1c....
20 1ZR8 - AJM C18 H22 N2 O2 C[N@]1c2cc....
21 1TH6 - OIN C17 H23 N O3 CN1[C@H]2C....
22 1Y38 - G3P C3 H9 O6 P C([C@H](CO....
23 3H1X Kd = 0.00000145 M IMN C19 H16 Cl N O4 Cc1c(c2cc(....
24 1SXK - BHA C7 H7 N O3 c1cc(c(cc1....
25 1TK4 - ALA ILE ARG SER n/a n/a
26 1SV3 - ANN C8 H8 O3 COc1ccc(cc....
27 2QHD - DAO C12 H24 O2 CCCCCCCCCC....
28 3BJW - SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
50% Homology Family (84)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 1U4J - MAN C6 H12 O6 C([C@@H]1[....
2 4YU7 - DHC C9 H8 O4 c1cc(c(cc1....
3 3MLM - MYR C14 H28 O2 CCCCCCCCCC....
4 3CXI - VIT C29 H50 O2 Cc1c(c2c(c....
5 1XXS - STE C18 H36 O2 CCCCCCCCCC....
6 3CYL - VIT C29 H50 O2 Cc1c(c2c(c....
7 6B81 - OCA C8 H16 O2 CCCCCCCC(=....
8 6DIK - GKP C22 H18 O12 c1c(cc(c(c....
9 6B80 - MYR C14 H28 O2 CCCCCCCCCC....
10 5VFJ Kd = 20 uM DHC C9 H8 O4 c1cc(c(cc1....
11 6B83 - 6NA C6 H12 O2 CCCCCC(=O)....
12 4YV5 Kd = 6.2 uM SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
13 4YZ7 - 9AR C17 H11 N O8 COc1c(ccc2....
14 3QNL - ROA C18 H16 O8 c1cc(c(cc1....
15 1Y4L - SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
16 1FDK - GLE C16 H32 F3 O6 P CCCCCCCCCC....
17 1MKV - GEL C20 H45 N O8 P2 CCCCCCCCOC....
18 2B96 - ANN C8 H8 O3 COc1ccc(cc....
19 5OW8 ic50 = 6.9 uM AYN C16 H11 F3 N2 O c1ccc2c(c1....
20 4UY1 ic50 = 20 uM TJM C10 H11 N3 O S Cc1cc(c(s1....
21 5OWC ic50 = 0.026 uM AYZ C19 H15 F3 N2 O4 c1cc(cc(c1....
22 5G3M ic50 = 24 uM 9JH C14 H13 N O c1ccc(cc1)....
23 2AZY - CHD C24 H40 O5 C[C@H](CCC....
24 1HN4 Kd = 0.15 mM MJI C22 H44 F3 O6 P CCCCCCCCCC....
25 2B01 - TUD C26 H45 N O6 S C[C@H](CCC....
26 1Y6O - MJI C22 H44 F3 O6 P CCCCCCCCCC....
27 2AZZ - TCH C26 H45 N O7 S C[C@H](CCC....
28 2B04 - CHO C26 H43 N O5 C[C@H](CCC....
29 2B00 - GCH C26 H43 N O6 C[C@H](CCC....
30 5P2P - DHG C20 H42 N O6 P CCCCCCCCCC....
31 3O4M - CAQ C6 H6 O2 c1ccc(c(c1....
32 2B03 - TUD C26 H45 N O6 S C[C@H](CCC....
33 1L8S - LPE C26 H57 N O6 P CCCCCCCCCC....
34 1FXF - MJI C22 H44 F3 O6 P CCCCCCCCCC....
35 1FX9 - MJI C22 H44 F3 O6 P CCCCCCCCCC....
36 3QLM Ki = 15.8 uM PLM C16 H32 O2 CCCCCCCCCC....
37 1POE - GEL C20 H45 N O8 P2 CCCCCCCCOC....
38 1DB4 - 8IN C21 H25 N2 O5 P Cc1c(c2cc(....
39 1KQU - BR4 C25 H33 N O3 c1ccc(cc1)....
40 5G3N ic50 = 0.012 uM X28 C23 H21 N O3 c1ccc(cc1)....
41 1KVO ic50 = 0.013 uM OAP C31 H37 N O3 S c1ccc(cc1)....
42 1J1A ic50 = 0.029 uM BHP C31 H37 N O4 c1ccc(cc1)....
43 6CE2 Kd = 0.5 uM SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
44 2QVD Kd = 0.00000145 M BER C20 H18 N O4 COc1ccc2cc....
45 1ZWP - NIM C13 H12 N2 O5 S CS(=O)(=O)....
46 1OXL - IDA C15 H18 N2 O3 CCCc1cc2cc....
47 1TG4 - PHE LEU ALA TYR LYS n/a n/a
48 1SKG - VAL ALA PHE ARG SER n/a n/a
49 1JQ9 Kd = 3.57 nM PHE LEU SER TYR LYS n/a n/a
50 2ARM Ki = 7.4 nM OIN C17 H23 N O3 CN1[C@H]2C....
51 1FV0 Kd = 1.18 uM 9AR C17 H11 N O8 COc1c(ccc2....
52 1Q7A Kd = 0.064 uM OPB C19 H20 N2 O3 CCCC[C@H]1....
53 1TG1 - PHQ LEU VAL ARG TYR n/a n/a
54 1ZYX - LCF C23 H22 Cl N O2 CC1(Cc2c(c....
55 1TJK - PHE LEU SER THR LYS n/a n/a
56 1KPM Ki = 1.59 uM VIT C29 H50 O2 Cc1c(c2c(c....
57 1TP2 - TDA C13 H26 O2 CCCCCCCCCC....
58 1TDV - TYR TRP ALA ALA ALA ALA n/a n/a
59 1TJ9 - VAL ALA ARG SER n/a n/a
60 1JQ8 Ki = 1.01 uM LEU ALA ILE TYR SER n/a n/a
61 1SQZ - PHQ ILE ALA ARG SER n/a n/a
62 1TGM - AIN C9 H8 O4 CC(=O)Oc1c....
63 1ZR8 - AJM C18 H22 N2 O2 C[N@]1c2cc....
64 1TH6 - OIN C17 H23 N O3 CN1[C@H]2C....
65 1Y38 - G3P C3 H9 O6 P C([C@H](CO....
66 3H1X Kd = 0.00000145 M IMN C19 H16 Cl N O4 Cc1c(c2cc(....
67 1SXK - BHA C7 H7 N O3 c1cc(c(cc1....
68 1TK4 - ALA ILE ARG SER n/a n/a
69 1SV3 - ANN C8 H8 O3 COc1ccc(cc....
70 5WZW ic50 = 1.23 uM U8D C22 H27 N2 O5 P CCc1c(c2cc....
71 5WZU ic50 = 0.1 uM 7W3 C21 H17 F3 N2 O5 Cc1c(c2c(n....
72 5WZT ic50 = 0.22 uM 7W6 C20 H17 Br N2 O5 Cc1c(c2c(n....
73 5WZS ic50 = 0.28 uM 7W9 C24 H20 N2 O5 Cc1c(c2c(n....
74 5Y5E - 7W3 C21 H17 F3 N2 O5 Cc1c(c2c(n....
75 5WZV ic50 = 0.21 uM 7W0 C26 H22 N2 O5 Cc1c(c2c(n....
76 6G5J ic50 = 15 nM EM8 C20 H17 F3 N2 O4 C[C@H](CC(....
77 2QHD - DAO C12 H24 O2 CCCCCCCCCC....
78 3BJW - SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
79 1S8G - DAO C12 H24 O2 CCCCCCCCCC....
80 1POB - GEL C20 H45 N O8 P2 CCCCCCCCOC....
81 1TD7 Kd = 43 uM NFL C13 H9 F3 N2 O2 c1cc(cc(c1....
82 1OXR Kd = 0.00000145 M AIN C9 H8 O4 CC(=O)Oc1c....
83 2WQ5 Kd = 180 uM MIY C23 H27 N3 O7 CN(C)c1ccc....
84 1MF4 Ki = 10.2 nM VAL ALA PHE ARG SER n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DAO; Similar ligands found: 62
No: Ligand ECFP6 Tc MDL keys Tc
1 MYR 1 1
2 EW8 1 1
3 TDA 1 1
4 F15 1 1
5 PLM 1 1
6 STE 1 1
7 X90 1 1
8 DAO 1 1
9 KNA 1 1
10 DCR 1 1
11 F23 1 1
12 11A 1 1
13 DKA 1 1
14 OCA 0.956522 1
15 SHV 0.833333 0.952381
16 KTC 0.793103 0.875
17 AZ1 0.73913 0.64
18 6NA 0.72 0.904762
19 ELA 0.71875 0.954545
20 OLA 0.71875 0.954545
21 NER 0.71875 0.954545
22 VCA 0.666667 0.954545
23 PAM 0.666667 0.954545
24 PML 0.625 0.6
25 3LA 0.606061 0.8
26 LEA 0.6 0.809524
27 MYZ 0.588235 0.909091
28 12H 0.586207 0.615385
29 ODD 0.567568 0.913043
30 BRC 0.566667 0.666667
31 14V 0.555556 0.740741
32 M12 0.545455 0.869565
33 14U 0.542857 0.703704
34 EIC 0.538462 0.913043
35 EOD 0.538462 0.7
36 D0G 0.5 0.954545
37 BMJ 0.5 0.954545
38 BNV 0.5 0.954545
39 BUA 0.48 0.666667
40 RCL 0.468085 0.84
41 FTT 0.459459 0.807692
42 HXD 0.459459 0.807692
43 56S 0.459459 0.653846
44 ODT 0.452381 0.782609
45 3X1 0.444444 0.818182
46 LNL 0.44186 0.826087
47 9J6 0.441176 0.666667
48 OOA 0.441176 0.76
49 CUY 0.435897 0.68
50 6UL 0.435897 0.68
51 CNS 0.435897 0.68
52 5UF 0.432432 0.807692
53 243 0.428571 0.807692
54 1QW 0.418605 0.606061
55 GYM 0.418605 0.606061
56 O8N 0.413793 0.75
57 1DO 0.413793 0.75
58 PL3 0.413793 0.75
59 OC9 0.413793 0.75
60 DE1 0.413793 0.75
61 F09 0.413793 0.75
62 T25 0.403846 0.677419
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2QHD; Ligand: DAO; Similar sites found with APoc: 88
This union binding pocket(no: 1) in the query (biounit: 2qhd.bio1) has 69 residues
No: Leader PDB Ligand Sequence Similarity
1 1NU4 MLA None
2 5N1X 8HH None
3 4LWU 20U None
4 1RV1 IMZ None
5 2BHW NEX None
6 3KP6 SAL None
7 4YEE 4CQ None
8 1SBR VIB None
9 4I67 G G G RPC None
10 1YYE 196 None
11 1U3R 338 None
12 3I6B KDO 1.63934
13 3AI3 SOE 1.63934
14 1M0S CIT 1.63934
15 1M2Z BOG 2.45902
16 3F81 STT 2.45902
17 5Z5I XYP 2.45902
18 5Y4R C2E 2.45902
19 1NHZ 486 2.45902
20 2Z8G GLC GLC BGC 2.45902
21 5AZC PGT 3.27869
22 1FX8 BOG 4.09836
23 5LX9 OLB 4.09836
24 6BR8 6OU 4.09836
25 2HHP FLC 4.09836
26 5LWY OLB 4.09836
27 4G9N NGA 4.09836
28 4HBM 0Y7 4.16667
29 3R5W F42 4.46429
30 4OGN 2U5 4.7619
31 4GN8 ASO 4.91803
32 5UNJ RJW 4.91803
33 5KJW 53C 4.91803
34 3BEO UDP 4.91803
35 5UC1 486 4.91803
36 4OAS 2SW 5.20833
37 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 5.7377
38 4RYV ZEA 5.7377
39 2JHP GUN 5.7377
40 1OHE ACE ALA SEP PRO 5.7377
41 3X01 AMP 5.7377
42 3AJ4 SEP 6.25
43 3TDC 0EU 6.55738
44 2BCG GER 6.55738
45 3KLL MAL 6.55738
46 1P9B HDA 6.55738
47 4GAH 0ET 6.55738
48 4OAR 2S0 6.55738
49 1ELI PYC 6.55738
50 4K90 MLA 6.55738
51 1E4I NFG 6.55738
52 5EY0 GTP 6.55738
53 4IA6 EIC 7.37705
54 6D5M FW4 7.37705
55 3FIU POP 7.37705
56 1ZX5 LFR 7.37705
57 1R6N 434 8.19672
58 2RH1 CLR 8.19672
59 5KK4 44E 8.33333
60 3MYZ TFX 9
61 1J78 OLA 9.01639
62 2XOC ADP 9.01639
63 4UCC ZKW 9.01639
64 1I58 ADP 9.01639
65 5C9J DAO 9.09091
66 2Y69 CHD 9.45946
67 5Z84 CHD 9.58904
68 5ZCO CHD 9.58904
69 5W97 CHD 9.58904
70 5W7B MYR 9.83607
71 1TV5 N8E 9.83607
72 1Z0N BCD 10.4167
73 4YSX E23 10.6557
74 2JC9 ADN 10.6557
75 5YRV 5AD 10.6557
76 6BYF CIT 11.4754
77 6BMS POV 11.4754
78 4TV1 36M 12.2951
79 2BJ4 OHT 12.2951
80 1W8S FBP 12.2951
81 3EYK EYK 12.2951
82 2QZO KN1 12.2951
83 5D9G GLU ASN LEU TYR PHE GLN 13.9344
84 2H7C SIA 13.9344
85 4OGQ 7PH 15.5738
86 6CB2 OLC 16.3934
87 3AQT RCO 17.2131
88 2WOR 2AN 24
Pocket No.: 2; Query (leader) PDB : 2QHD; Ligand: DAO; Similar sites found with APoc: 21
This union binding pocket(no: 2) in the query (biounit: 2qhd.bio1) has 68 residues
No: Leader PDB Ligand Sequence Similarity
1 1DTL BEP None
2 1LNX URI None
3 4M7F BM3 None
4 4NTO 1PW None
5 3IX9 MTX None
6 1NF8 BOG 3.27869
7 1ZED PNP 3.27869
8 4ZDJ UTP 3.27869
9 3B6C SDN 4.09836
10 6C0B MLI 4.09836
11 4LIK CIT 4.09836
12 2GWH PCI 4.91803
13 4WBD CIT 4.91803
14 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 4.91803
15 1YXM ADE 4.91803
16 4G86 BNT 5.7377
17 6C1R EFD 8.19672
18 3DLS ADP 9.83607
19 2V7Q ADP 10.6557
20 1XKV ATP 11.4754
21 1D8C SOR 12.2951
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