Receptor
PDB id Resolution Class Description Source Keywords
5L92 2.1 Å NON-ENZYME: OTHER THE 2.1 A CRYSTAL STRUCTURE OF CYP109E1 FROM BACILLUS MEGATE COMPLEX WITH CORTICOSTERONE BACILLUS MEGATERIUM (STRAIN DSM 319) BACILLUS BACTERIAL PROTEINS BINDING SITES CATALYSIS CORTICOSTERONE CYTOCHROME P-450 ENZYME SYSTEM CYTOCHROME HYDROXYLATION ESCHERICHIA COLI HEME LIGANDS MOLECULAR SOXIDATION-REDUCTION OXYGEN PROTEIN PROTEIN STRUCTURE SESTEROIDS SUBSTRATE SPECIFICITY OXIDOREDUCTASE
Ref.: STRUCTURAL BASIS OF STEROID BINDING AND OXIDATION B CYTOCHROME P450 CYP109E1 FROM BACILLUS MEGATERIUM. FEBS J. V. 283 4128 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
HEM A:501;
B:501;
Part of Protein;
Part of Protein;
none;
none;
submit data
616.487 C34 H32 Fe N4 O4 Cc1c2...
C0R A:502;
Valid;
none;
Kd = 91 uM
346.461 C21 H30 O4 C[C@]...
MLA A:503;
Valid;
none;
submit data
104.061 C3 H4 O4 C(C(=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5L92 2.1 Å NON-ENZYME: OTHER THE 2.1 A CRYSTAL STRUCTURE OF CYP109E1 FROM BACILLUS MEGATE COMPLEX WITH CORTICOSTERONE BACILLUS MEGATERIUM (STRAIN DSM 319) BACILLUS BACTERIAL PROTEINS BINDING SITES CATALYSIS CORTICOSTERONE CYTOCHROME P-450 ENZYME SYSTEM CYTOCHROME HYDROXYLATION ESCHERICHIA COLI HEME LIGANDS MOLECULAR SOXIDATION-REDUCTION OXYGEN PROTEIN PROTEIN STRUCTURE SESTEROIDS SUBSTRATE SPECIFICITY OXIDOREDUCTASE
Ref.: STRUCTURAL BASIS OF STEROID BINDING AND OXIDATION B CYTOCHROME P450 CYP109E1 FROM BACILLUS MEGATERIUM. FEBS J. V. 283 4128 2016
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 5L92 Kd = 91 uM C0R C21 H30 O4 C[C@]12CCC....
2 5L91 Kd = 91 uM C0R C21 H30 O4 C[C@]12CCC....
3 5L94 Kd = 105 uM TES C19 H28 O2 C[C@]12CC[....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 5L92 Kd = 91 uM C0R C21 H30 O4 C[C@]12CCC....
2 5L91 Kd = 91 uM C0R C21 H30 O4 C[C@]12CCC....
3 5L94 Kd = 105 uM TES C19 H28 O2 C[C@]12CC[....
50% Homology Family (53)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 3A50 - VD3 C27 H44 O CC(C)CCC[C....
2 3A51 - VDY C27 H44 O2 C[C@H](CCC....
3 5FOI Kd = 1 nM MY8 C29 H49 N O6 CC[C@@H]1[....
4 4J6C - STR C21 H30 O2 CC(=O)[C@H....
5 4JBT - ASD C19 H26 O2 C[C@]12CCC....
6 4J6B - PLO C21 H32 O2 CC(=O)[C@H....
7 4J6D - TES C19 H28 O2 C[C@]12CC[....
8 4UBS Kd = 65 uM DIF C14 H11 Cl2 N O2 c1ccc(c(c1....
9 5L1W Kd = 31 uM 7PF C15 H18 O5 CC1(C[C@H]....
10 5L1O Kd = 7.2 uM 7PF C15 H18 O5 CC1(C[C@H]....
11 5L1U Kd = 340 uM 7PF C15 H18 O5 CC1(C[C@H]....
12 5L1S Kd = 160 uM 7PF C15 H18 O5 CC1(C[C@H]....
13 5L1V Kd = 43 uM 7PF C15 H18 O5 CC1(C[C@H]....
14 5L1Q Kd = 170 uM 7DF C15 H20 O5 CC1(C[C@H]....
15 5L1P - 7PT C15 H16 O5 C[C@H]1[C@....
16 2NZ5 Kd = 10.5 uM 226 C10 H8 O5 c1c(cc(c2c....
17 3ABA - FLI C35 H58 O9 CCCCCC[C@@....
18 5IT1 - 2OH C15 H16 O2 CC(C)(c1cc....
19 2C7X - NRB C28 H47 N O7 CC[C@@H]1[....
20 2C6H - PXI C25 H43 N O6 CC[C@@H]1[....
21 2CD8 - PXI C25 H43 N O6 CC[C@@H]1[....
22 2WI9 Kd = 309 uM 1D2 C20 H39 N O3 C[C@@H]1C[....
23 2VZM Kd = 171.9 uM NRB C28 H47 N O7 CC[C@@H]1[....
24 4B7S Kd = 81 uM QLE C22 H37 N O5 CC[C@@H]1[....
25 3ZK5 Kd = 118 uM Z18 C21 H35 N O5 CC[C@@H]1[....
26 5X7E - 7ZU C28 H44 O3 C[C@H](/C=....
27 2ZBZ - VDX C27 H44 O3 C[C@H](CCC....
28 3CV9 - VDX C27 H44 O3 C[C@H](CCC....
29 2XBK Kd = 4 uM XBK C33 H47 N O12 C[C@@H]1CC....
30 1EUP - ASD C19 H26 O2 C[C@]12CCC....
31 1EGY - 9AP C14 H11 N c1ccc2c(c1....
32 1JIP - KTN C26 H28 Cl2 N4 O4 CC(=O)N1CC....
33 1Z8Q - DEB C21 H38 O6 CC[C@@H]1[....
34 1Z8P - DEB C21 H38 O6 CC[C@@H]1[....
35 1JIN - KTN C26 H28 Cl2 N4 O4 CC(=O)N1CC....
36 1JIO - DEB C21 H38 O6 CC[C@@H]1[....
37 1Z8O - DEB C21 H38 O6 CC[C@@H]1[....
38 1S1F - PIM C9 H8 N2 c1ccc(cc1)....
39 2D09 Kd = 7.3 uM FLV C10 H6 O5 c1c(cc(c2c....
40 1T93 - FLV C10 H6 O5 c1c(cc(c2c....
41 2D0E Kd = 43 uM NQ C10 H6 O3 c1ccc2c(c1....
42 1XQD Kd = 0.07 mM DND C21 H27 N6 O15 P2 c1cc(c[n+]....
43 5L92 Kd = 91 uM C0R C21 H30 O4 C[C@]12CCC....
44 5L91 Kd = 91 uM C0R C21 H30 O4 C[C@]12CCC....
45 5L94 Kd = 105 uM TES C19 H28 O2 C[C@]12CC[....
46 4AW3 - MYV C37 H61 N O12 CC[C@@H]1[....
47 2Y5N - MYV C37 H61 N O12 CC[C@@H]1[....
48 3ZSN - MIV C37 H61 N O11 CC[C@@H]1[....
49 2Y98 - MIV C37 H61 N O11 CC[C@@H]1[....
50 2Y5Z - ZM3 C36 H59 N O11 CC[C@@H]1[....
51 2YCA - ZM3 C36 H59 N O11 CC[C@@H]1[....
52 2Y46 - MIV C37 H61 N O11 CC[C@@H]1[....
53 3WVS - RRM C32 H48 O7 CCCC[C@H]1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: C0R; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 C0R 1 1
2 AS4 0.647059 0.97619
3 1CA 0.552941 0.952381
4 HCY 0.551724 0.933333
5 STR 0.411111 0.738095
Ligand no: 2; Ligand: MLA; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 MLA 1 1
2 AAE 0.6 0.631579
3 98J 0.428571 0.608696
4 0L1 0.411765 0.619048
5 GUA 0.411765 0.65
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5L92; Ligand: MLA; Similar sites found: 29
This union binding pocket(no: 1) in the query (biounit: 5l92.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2HFU MEV 0.02425 0.40911 3.91566
2 2X1L MET 0.0208 0.41235 6.09756
3 5V49 MET 0.01852 0.40948 6.58537
4 4MGA 27L 0.01099 0.42537 6.66667
5 2CI5 HCS 0.02263 0.41005 6.69014
6 4MRP GSH 0.01369 0.4197 7.31707
7 5UC9 MYR 0.02577 0.40779 9.73451
8 4DVQ 1CA 0.01962 0.4082 10.7317
9 3V1S 0LH 0.006518 0.43484 15.8385
10 2NNJ 225 0.01489 0.41431 16.1765
11 3MDV CL6 0.006527 0.40724 20.4878
12 2HI4 BHF 0.004043 0.42131 22.9268
13 4RQL SNE 0.009336 0.42458 23.4146
14 2FDW D3G 0.004792 0.43924 25.8537
15 4NKW PLO 0.001719 0.40343 29.7561
16 2VE3 REA 0.01569 0.40903 34.3902
17 1ZOA 140 0.01115 0.40185 36.3415
18 1RE9 DSO 0.002905 0.4005 37.8049
19 4JX1 CAM 0.002119 0.44618 38.0488
20 4JX1 CAH 0.002575 0.44444 38.0488
21 3WEC AUI 0.01236 0.40285 41.9512
22 2WH8 II2 0.01315 0.41704 44.878
23 1Q5D EPB 0.001814 0.42913 45.3659
24 4L77 CNL 0.00117 0.47606 46.9849
25 2X5W K2B 0.001986 0.40742 47.0732
26 2Z3U CRR 0.0002609 0.41992 47.5294
27 2WM4 VGJ 0.0002404 0.47634 47.561
28 2XFH CL6 0.0002883 0.42922 47.561
29 2YOO K2B 0.001888 0.43219 47.6658
Pocket No.: 2; Query (leader) PDB : 5L92; Ligand: C0R; Similar sites found: 39
This union binding pocket(no: 2) in the query (biounit: 5l92.bio1) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WG0 CHD 0.023 0.41364 None
2 4XDY HIO 0.02417 0.41556 1.77515
3 1A05 IPM 0.03566 0.40848 1.95531
4 3UU7 2OH 0.03893 0.40337 2.78884
5 4PSR FUL 0.03856 0.40011 3.17073
6 3LA3 2FT 0.03406 0.40816 3.29218
7 2WR1 NAG 0.002505 0.49415 3.65854
8 2W9S TOP 0.04433 0.40041 3.72671
9 1YRO UDP 0.02622 0.4186 4.1958
10 4RW3 PLM 0.01107 0.44414 4.30464
11 3ZJQ NCA 0.03111 0.40868 4.61538
12 2B3B GLC 0.03205 0.40393 4.75
13 2X1L MET 0.02298 0.41622 6.09756
14 5V49 MET 0.02138 0.4131 6.58537
15 2CI5 HCS 0.02859 0.41097 6.69014
16 4MRP GSH 0.01777 0.4197 7.31707
17 5UC9 MYR 0.02121 0.40561 9.73451
18 4DVQ 1CA 0.02692 0.40789 10.7317
19 3NA0 2DC 0.01432 0.40041 14.3902
20 3V1S 0LH 0.00887 0.43038 15.8385
21 2NNJ 225 0.01719 0.41802 16.1765
22 3TIK JKF 0.01446 0.41016 19.0244
23 1N6B DMZ 0.002997 0.43885 19.7561
24 2HI4 BHF 0.004981 0.4247 22.9268
25 4RQL SNE 0.01285 0.42458 23.4146
26 2FDW D3G 0.006692 0.43924 25.8537
27 2VE3 REA 0.01913 0.4116 34.3902
28 1RE9 DSO 0.005428 0.40114 37.8049
29 4JX1 CAM 0.002874 0.44618 38.0488
30 4JX1 CAH 0.00348 0.44444 38.0488
31 3WEC AUI 0.01906 0.401 41.9512
32 2WH8 II2 0.001985 0.46645 44.878
33 1Q5D EPB 0.002743 0.42913 45.3659
34 4L77 CNL 0.001486 0.47871 46.9849
35 2X5W K2B 0.0004127 0.44607 47.0732
36 2Z3U CRR 0.0008144 0.42017 47.5294
37 2WM4 VGJ 0.0003747 0.47634 47.561
38 2XFH CL6 0.0001102 0.46153 47.561
39 2YOO K2B 0.0005919 0.46276 47.6658
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