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Receptor
PDB id Resolution Class Description Source Keywords
3WIX 1.9 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF MCL-1 IN COMPLEX WITH COMPOUND 4 HOMO SAPIENS REGULATION APOPTOSIS
Ref.: DISCOVERY OF POTENT MCL-1/BCL-XL DUAL INHIBITORS BY HYBRIDIZATION STRATEGY BASED ON STRUCTURAL ANALYSIS TARGET PROTEINS. J.MED.CHEM. V. 56 9635 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
LC3 D:501;
C:501;
A:501;
B:501;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
ic50 = 0.54 uM
466.485 C28 H22 N2 O5 c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5IF4 2.39 Å NON-ENZYME: OTHER DISCOVERY OF POTENT MYELOID CELL LEUKEMIA-1 (MCL-1) INHIBITO STRUCTURE-BASED DESIGN HOMO SAPIENS MYELOID CELL LEUKEMIA-1 BCL-2 APOPTOSIS APOPTOSIS-APOPTOSINHIBITOR COMPLEX
Ref.: DISCOVERY AND BIOLOGICAL CHARACTERIZATION OF POTENT CELL LEUKEMIA-1 INHIBITORS. FEBS LETT. V. 591 240 2017
Members (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 5IF4 Ki < 1 nM 6AK C39 H39 Cl2 N5 O4 Cc1cc(cc(c....
2 6B4U Ki = 0.009 uM CN7 C35 H36 N2 O4 Cc1ccccc1c....
3 4WMR - 865 C37 H36 N6 O4 Cc1ccnc(c1....
4 4OQ6 ic50 = 3.3 uM 2UV C16 H16 O3 CCCc1ccc(c....
5 3WIY ic50 = 0.61 uM LC6 C47 H46 N6 O8 S2 Cc1cc(ccc1....
6 5VKC - 9EA C46 H46 N6 O5 Cc1c(c(nn1....
7 5FC4 Ki = 231 nM 5WL C23 H21 Cl N2 O4 S CS(=O)(=O)....
8 6FS1 Kd = 0.098 uM E4Q C34 H35 N5 O3 S Cc1cc(nn1C....
9 3WIX ic50 = 0.54 uM LC3 C28 H22 N2 O5 c1ccc2c(c1....
10 6B4L Ki = 0.34 uM CJY C22 H19 N O3 c1ccc2c(c1....
11 4HW3 Ki = 0.32 uM 19G C20 H19 Cl O3 S Cc1cc(cc(c....
12 5KU9 ic50 = 1.49 uM 6XJ C33 H36 Br Cl2 N5 O4 CNC(=O)C[C....
13 4ZBI Ki = 0.31 uM 4M6 C25 H23 N O3 c1ccc2c(c1....
14 4ZBF Ki = 0.074 uM 4M7 C25 H23 N O4 S c1ccc2c(c1....
70% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 5IF4 Ki < 1 nM 6AK C39 H39 Cl2 N5 O4 Cc1cc(cc(c....
2 6B4U Ki = 0.009 uM CN7 C35 H36 N2 O4 Cc1ccccc1c....
3 4WMR - 865 C37 H36 N6 O4 Cc1ccnc(c1....
4 4OQ6 ic50 = 3.3 uM 2UV C16 H16 O3 CCCc1ccc(c....
5 3WIY ic50 = 0.61 uM LC6 C47 H46 N6 O8 S2 Cc1cc(ccc1....
6 5VKC - 9EA C46 H46 N6 O5 Cc1c(c(nn1....
7 5FC4 Ki = 231 nM 5WL C23 H21 Cl N2 O4 S CS(=O)(=O)....
8 6FS1 Kd = 0.098 uM E4Q C34 H35 N5 O3 S Cc1cc(nn1C....
9 3WIX ic50 = 0.54 uM LC3 C28 H22 N2 O5 c1ccc2c(c1....
10 6B4L Ki = 0.34 uM CJY C22 H19 N O3 c1ccc2c(c1....
11 4HW3 Ki = 0.32 uM 19G C20 H19 Cl O3 S Cc1cc(cc(c....
12 5KU9 ic50 = 1.49 uM 6XJ C33 H36 Br Cl2 N5 O4 CNC(=O)C[C....
13 4ZBI Ki = 0.31 uM 4M6 C25 H23 N O3 c1ccc2c(c1....
14 4ZBF Ki = 0.074 uM 4M7 C25 H23 N O4 S c1ccc2c(c1....
50% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 5IF4 Ki < 1 nM 6AK C39 H39 Cl2 N5 O4 Cc1cc(cc(c....
2 6B4U Ki = 0.009 uM CN7 C35 H36 N2 O4 Cc1ccccc1c....
3 4WMR - 865 C37 H36 N6 O4 Cc1ccnc(c1....
4 4OQ6 ic50 = 3.3 uM 2UV C16 H16 O3 CCCc1ccc(c....
5 3WIY ic50 = 0.61 uM LC6 C47 H46 N6 O8 S2 Cc1cc(ccc1....
6 5VKC - 9EA C46 H46 N6 O5 Cc1c(c(nn1....
7 5FC4 Ki = 231 nM 5WL C23 H21 Cl N2 O4 S CS(=O)(=O)....
8 6FS1 Kd = 0.098 uM E4Q C34 H35 N5 O3 S Cc1cc(nn1C....
9 3WIX ic50 = 0.54 uM LC3 C28 H22 N2 O5 c1ccc2c(c1....
10 6B4L Ki = 0.34 uM CJY C22 H19 N O3 c1ccc2c(c1....
11 4HW3 Ki = 0.32 uM 19G C20 H19 Cl O3 S Cc1cc(cc(c....
12 5KU9 ic50 = 1.49 uM 6XJ C33 H36 Br Cl2 N5 O4 CNC(=O)C[C....
13 4ZBI Ki = 0.31 uM 4M6 C25 H23 N O3 c1ccc2c(c1....
14 4ZBF Ki = 0.074 uM 4M7 C25 H23 N O4 S c1ccc2c(c1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: LC3; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 LC3 1 1
2 CJY 0.46875 0.666667
3 4M6 0.425926 0.683333
4 4M7 0.4 0.619718
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5IF4; Ligand: 6AK; Similar sites found with APoc: 149
This union binding pocket(no: 1) in the query (biounit: 5if4.bio2) has 59 residues
No: Leader PDB Ligand Sequence Similarity
1 4XCP PLM None
2 3KP6 SAL None
3 3RET SAL None
4 3RET PYR None
5 4YDX TCE None
6 4V2O CLQ None
7 5UGW GSH None
8 1ECM TSA None
9 5X80 SAL None
10 3IA4 MTX None
11 1L0I PSR None
12 1UO5 PIH None
13 4B1X LAB None
14 1N9L FMN None
15 1MID LAP None
16 3KPE TM3 None
17 1ZEI CRS None
18 1HBK MYR None
19 3G4Q MCH None
20 4V1F BQ1 None
21 5AZC PGT 1.25786
22 2HFN FMN 1.30719
23 2Z6D FMN 1.53846
24 1N8V BDD 1.78571
25 5OLK DTP 1.88679
26 1KSK URA 1.88679
27 2Z9I GLY ALA THR VAL 2.51572
28 6BWL UDP 2.51572
29 3ET1 ET1 2.51572
30 5Y02 HBX 2.80374
31 1JGS SAL 2.89855
32 2WG9 OCA 3.07692
33 4IBF 1D5 3.10078
34 1DTL BEP 3.14465
35 1SJD NPG 3.14465
36 2GN2 C5P 3.14465
37 5CX6 CDP 3.14465
38 2HJ9 AI2 3.14465
39 1JX6 AI2 3.14465
40 4M5P 23W 3.14465
41 2Y65 ADP 3.14465
42 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 3.77358
43 3E70 GDP 3.77358
44 4WGF HX2 3.77358
45 3FAL REA 3.77358
46 1M2Z BOG 3.77358
47 1SR7 MOF 3.77358
48 4OR7 25U 3.77358
49 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 3.80952
50 2HPL ASP ASP LEU TYR GLY 4
51 5XJ7 87O 4.40252
52 4DE3 DN8 4.40252
53 1XMY ROL 4.40252
54 4UBS DIF 4.40252
55 2E9L PLM 4.40252
56 1XM4 PIL 4.40252
57 1XMU ROF 4.40252
58 5Y80 IRE 4.72973
59 1YKD CMP 4.77387
60 5NM7 GLY 5.03145
61 5KD8 TNR 5.03145
62 2BCG GER 5.03145
63 3B9Z CO2 5.03145
64 1Q19 SSC 5.03145
65 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 5.03145
66 6CB2 OLC 5.03145
67 6G5Q EMZ 5.03145
68 1QH8 HCA 5.03145
69 3ROE THM 5.03145
70 2WKQ FMN 5.03145
71 3N7S 3N7 5.21739
72 4EJ1 FOL 5.22388
73 4WUJ FMN 5.44218
74 5OCA 9QZ 5.66038
75 1CZA ADP 5.66038
76 4WQ2 3SU 5.66038
77 3DTU DXC 5.66038
78 4COL DTP 5.66038
79 4OGQ 1O2 6.28931
80 1XQP 8HG 6.28931
81 3HP9 CF1 6.28931
82 5KTQ DCP 6.28931
83 5MZI FYK 6.28931
84 2GBB CIT 6.41026
85 4F4S EFO 6.57895
86 6EVN PRO PRO GLY PRO ALA GLY PRO PRO GLY 6.86275
87 3CV2 COA 6.91824
88 2F7A BEZ 6.91824
89 5O0J 8BR 6.91824
90 5LX9 OLB 6.91824
91 3F8C HT1 7.14286
92 4XDA ADP 7.54717
93 3E3U NVC 7.54717
94 5JOG 6LT 7.54717
95 4O4Z N2O 7.79221
96 4R38 RBF 7.85714
97 3TL1 JRO 8.1761
98 1NU4 MLA 8.24742
99 5CHR 4NC 8.75912
100 1R6N 434 8.80503
101 1NF8 BOG 8.80503
102 3RLF MAL 8.80503
103 5A4W QCT 8.80503
104 2Q8G AZX 9.43396
105 5IM3 DTP 9.43396
106 5C1M OLC 9.6
107 5C1M CLR 9.6
108 2BHW NEX 10.0629
109 3KLL MAL 10.0629
110 2BHW XAT 10.0629
111 3TDC 0EU 10.6918
112 3WXL ADP 10.6918
113 6CS8 F9Y 10.6918
114 4EIL FOL 10.6918
115 5X13 HC4 10.6918
116 5K53 STE 10.6918
117 6BVI EC4 10.7784
118 6BVL EBY 10.7784
119 6BVK EAV 10.7784
120 6BVM EBV 10.7784
121 6BVJ EAS 10.7784
122 2FP2 TSA 11.3208
123 1ZED PNP 11.9497
124 1D1G MTX 11.9497
125 2WH8 II2 11.9497
126 3SQP 3J8 11.9497
127 2Y69 CHD 12.5
128 5M36 9SZ 12.5786
129 1W6U HXC 13.2075
130 5V3Y 5V8 13.2075
131 6AYI C3G 13.8365
132 4IA6 EIC 14.4654
133 1TV5 N8E 15.0943
134 5U83 ZN8 16.3522
135 5Z84 CHD 17.8571
136 5ZCO CHD 17.8571
137 5W97 CHD 17.8571
138 5N6N SUC 20.1258
139 3W54 RNB 20.7547
140 5W7B MYR 21.9858
141 4MGA 27L 24.5283
142 4MG9 27K 24.5283
143 4TV1 36M 24.5283
144 5DX3 EST 24.5283
145 3UUA 0CZ 24.5283
146 1M48 FRG 28.5714
147 3QKD HI0 35.8491
148 2W3L DRO 40.9722
149 6GL8 F3Q 44.0252
Pocket No.: 2; Query (leader) PDB : 5IF4; Ligand: 6AK; Similar sites found with APoc: 63
This union binding pocket(no: 2) in the query (biounit: 5if4.bio1) has 37 residues
No: Leader PDB Ligand Sequence Similarity
1 1UO4 PIH None
2 4ZGM 32M None
3 4I67 G G G RPC None
4 5ZZB LAB None
5 1FWV SGA MAG FUC None
6 2B96 ANN None
7 4OB6 S2T 1.88679
8 2PX6 DH9 1.88679
9 1S9D AFB 1.88679
10 2OFW ADX 2.51572
11 3SP6 IL2 2.51572
12 5Y02 MXN 2.80374
13 2PR5 FMN 3.0303
14 2Y7P SAL 3.14465
15 1JPA ANP 3.77358
16 1DKF BMS 3.77358
17 3P7N FMN 3.77358
18 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 4.40252
19 4BNU 9KQ 4.40252
20 2YFB SIN 4.40252
21 5YEE LAB 4.41176
22 6BMS POV 5.03145
23 4OKS 2T9 5.03145
24 2OKL BB2 5.03145
25 2FSH ANP 5.03145
26 1OW4 2AN 5.42636
27 1J78 OLA 5.66038
28 4XPL ACO 5.66038
29 5CQG 55C 5.66038
30 4GCZ FMN 5.66038
31 4OGQ UMQ 6.28931
32 4OGQ 7PH 6.28931
33 5EE7 5MV 6.28931
34 3KIF GDL 6.60377
35 1T5C ADP 6.91824
36 5L2R MLA 6.91824
37 1ZGA HMK 6.91824
38 3T50 FMN 7.03125
39 2D5X L35 7.53425
40 5L7G LYS SER LEU LEU GLN GLN LEU LEU THR GLU 8.1761
41 2WPX ACO 8.1761
42 2HHP FLC 8.80503
43 5LWY OLB 9.2437
44 1RV1 IMZ 9.41177
45 1VR0 3SL 9.43396
46 2ZR9 DTP 9.43396
47 1SBR VIB 10.0629
48 4I90 CHT 10.6918
49 1OYY AGS 11.3208
50 4YC9 4C1 11.9497
51 6GBV FMN 12.3288
52 5M37 9SZ 12.5786
53 2PRG BRL 12.5786
54 3T03 3T0 12.5786
55 3B1M KRC 12.5786
56 1RDT 570 12.5786
57 4D52 GXL 12.5786
58 5V03 658 12.7451
59 4YSX E23 14.7436
60 2GJ5 VD3 17.6101
61 5ZCO PEK 17.8571
62 5A86 D7E 19.4969
63 2BJ4 OHT 24.5283
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