Receptor
PDB id Resolution Class Description Source Keywords
2ZBZ 1.9 Å EC: 1.14.15.- CRYSTAL STRUCTURE OF VITAMIN D HYDROXYLASE CYTOCHROME P450 105A1 (R84A MUTANT) IN COMPLEX WITH 1,25-DIHYDROXYVITAMIN D 3 STREPTOMYCES GRISEOLUS P450 BETA PRISM HEME IRON METAL-BINDING MONOOXYGENASE OXIDOREDUCTASE
Ref.: CRYSTAL STRUCTURE OF CYP105A1 (P450SU-1) IN COMPLEX WITH 1ALPHA,25-DIHYDROXYVITAMIN D3 BIOCHEMISTRY V. 47 4017 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
HEM A:413;
 Part of Protein;
 none;
 submit data
616.487 C34 H32 Fe N4 O4 Cc1c2...
VDX A:501;
 Valid;
 none;
 submit data
416.636 C27 H44 O3 C[C@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3CV9 1.7 Å EC: 1.14.15.- CRYSTAL STRUCTURE OF VITAMIN D HYDROXYLASE CYTOCHROME P450 105A1 (R73A/R84A MUTANT) IN COMPLEX WITH 1ALPHA,25- D IHYDROXYVITAMIN D3 STREPTOMYCES GRISEOLUS P450 BETA PRISM HEME IRON METAL-BINDING MONOOXYGENASE OXIDOREDUCTASE
Ref.: STRUCTURE-BASED DESIGN OF A HIGHLY ACTIVE VITAMIN D HYDROXYLASE FROM STREPTOMYCES GRISEOLUS CYP105A1 BIOCHEMISTRY V. 47 11964 2008
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5X7E - 7ZU C28 H44 O3 C[C@H](/C=....
2 2ZBZ - VDX C27 H44 O3 C[C@H](CCC....
3 3CV9 - VDX C27 H44 O3 C[C@H](CCC....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5X7E - 7ZU C28 H44 O3 C[C@H](/C=....
2 2ZBZ - VDX C27 H44 O3 C[C@H](CCC....
3 3CV9 - VDX C27 H44 O3 C[C@H](CCC....
50% Homology Family (53)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 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 5GWE Kd = 62 uM GWM C7 H9 O4 P Cc1ccc(cc1....
5 5XJN - 88L C8 H11 O4 P CCc1ccc(cc....
6 4OQR Kd = 29.3 uM 2UO C23 H34 O5 CC[C@H](C)....
7 4UBS Kd = 65 uM DIF C14 H11 Cl2 N O2 c1ccc(c(c1....
8 5L1O Kd = 7.2 uM 7PF C15 H18 O5 CC1(C[C@H]....
9 5L1U Kd = 340 uM 7PF C15 H18 O5 CC1(C[C@H]....
10 5L1S Kd = 160 uM 7PF C15 H18 O5 CC1(C[C@H]....
11 5L1V Kd = 43 uM 7PF C15 H18 O5 CC1(C[C@H]....
12 5L1Q Kd = 170 uM 7DF C15 H20 O5 CC1(C[C@H]....
13 5L1P - 7PT C15 H16 O5 C[C@H]1[C@....
14 2NZ5 Kd = 10.5 uM 226 C10 H8 O5 c1c(cc(c2c....
15 5IT1 - 2OH C15 H16 O2 CC(C)(c1cc....
16 2WI9 Kd = 309 uM 1D2 C20 H39 N O3 C[C@@H]1C[....
17 2VZM Kd = 171.9 uM NRB C28 H47 N O7 CC[C@@H]1[....
18 4B7S Kd = 81 uM QLE C22 H37 N O5 CC[C@@H]1[....
19 3ZK5 Kd = 118 uM Z18 C21 H35 N O5 CC[C@@H]1[....
20 5X7E - 7ZU C28 H44 O3 C[C@H](/C=....
21 2ZBZ - VDX C27 H44 O3 C[C@H](CCC....
22 3CV9 - VDX C27 H44 O3 C[C@H](CCC....
23 2XBK Kd = 4 uM XBK C33 H47 N O12 C[C@@H]1CC....
24 6ZI7 - QR8 C20 H36 O6 C[C@H]1C[C....
25 6ZHZ - QR8 C20 H36 O6 C[C@H]1C[C....
26 6ZI3 - DEB C21 H38 O6 CC[C@@H]1[....
27 6M4P - F4O C40 H53 N O14 Cc1c2c(c3c....
28 1Z8Q - DEB C21 H38 O6 CC[C@@H]1[....
29 1Z8P - DEB C21 H38 O6 CC[C@@H]1[....
30 1JIN - KTN C26 H28 Cl2 N4 O4 CC(=O)N1CC....
31 1JIO - DEB C21 H38 O6 CC[C@@H]1[....
32 1Z8O - DEB C21 H38 O6 CC[C@@H]1[....
33 1S1F - PIM C9 H8 N2 c1ccc(cc1)....
34 2D09 Kd = 7.3 uM FLV C10 H6 O5 c1c(cc(c2c....
35 1T93 - FLV C10 H6 O5 c1c(cc(c2c....
36 2D0E Kd = 43 uM NQ C10 H6 O3 c1ccc2c(c1....
37 1XQD Kd = 0.07 mM DND C21 H27 N6 O15 P2 c1cc(c[n+]....
38 6GK6 Kd = 2.1 uM MYR C14 H28 O2 CCCCCCCCCC....
39 5L91 Kd = 91 uM C0R C21 H30 O4 C[C@]12CCC....
40 5L94 Kd = 105 uM TES C19 H28 O2 C[C@]12CC[....
41 4AW3 - MYV C37 H61 N O12 CC[C@@H]1[....
42 2Y5N - MYV C37 H61 N O12 CC[C@@H]1[....
43 3ZSN - MIV C37 H61 N O11 CC[C@@H]1[....
44 2Y98 - MIV C37 H61 N O11 CC[C@@H]1[....
45 2Y5Z - ZM3 C36 H59 N O11 CC[C@@H]1[....
46 2YCA - ZM3 C36 H59 N O11 CC[C@@H]1[....
47 2Y46 - MIV C37 H61 N O11 CC[C@@H]1[....
48 3WVS - RRM C32 H48 O7 CCCC[C@H]1....
49 6TO2 Kd = 20 nM NQ8 C19 H30 O C[C@@]12CC....
50 4J6C - STR C21 H30 O2 CC(=O)[C@H....
51 4JBT - ASD C19 H26 O2 C[C@]12CCC....
52 4J6B - PLO C21 H32 O2 CC(=O)[C@H....
53 4J6D - TES C19 H28 O2 C[C@]12CC[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: VDX; Similar ligands found: 48
No: Ligand ECFP6 Tc MDL keys Tc
1 VDX 1 1
2 BIV 0.758621 1
3 MVD 0.714286 1
4 VDY 0.712644 0.926829
5 M7E 0.693878 0.672414
6 VDZ 0.674157 1
7 YSV 0.674157 1
8 C33 0.659794 0.97619
9 ZNE 0.656863 0.754717
10 VD2 0.655556 0.97561
11 O1C 0.653061 0.931818
12 C3O 0.646465 0.891304
13 7ZU 0.641304 0.951219
14 OCC 0.633663 0.87234
15 TEJ 0.628866 0.847826
16 JC1 0.625 0.888889
17 MC9 0.623656 0.904762
18 91W 0.614583 0.866667
19 KH1 0.61 0.888889
20 8J3 0.607843 0.906977
21 8J0 0.607843 0.906977
22 EB1 0.6 0.928571
23 FMV 0.58 0.829787
24 TEY 0.576577 0.621212
25 ICJ 0.572816 0.97619
26 6VH 0.567308 0.833333
27 YS3 0.553191 0.97561
28 VD3 0.553191 0.853659
29 YS2 0.542553 0.909091
30 VDP 0.520661 0.634921
31 AKX 0.518519 0.930233
32 YSD 0.50505 0.928571
33 ZYD 0.50505 1
34 0CO 0.5 0.851064
35 COV 0.5 0.851064
36 VD1 0.463158 0.904762
37 TX5 0.455446 0.904762
38 8BL 0.446429 0.909091
39 8BO 0.442478 0.888889
40 9RO 0.442478 0.888889
41 G72 0.4375 0.851064
42 H97 0.4375 0.851064
43 YA1 0.435185 0.97619
44 YI3 0.425926 0.952381
45 AYT 0.419048 0.926829
46 YI4 0.405405 0.909091
47 TKA 0.403509 0.906977
48 TK3 0.401709 0.906977
Similar Ligands (3D)
Ligand no: 1; Ligand: VDX; Similar ligands found: 9
No: Ligand Similarity coefficient
1 VD4 0.9544
2 2MV 0.9456
3 23R 0.9333
4 B0B 0.9141
5 AYK 0.9083
6 CA9 0.8970
7 VD5 0.8944
8 E05 0.8839
9 9KX 0.8607
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3CV9; Ligand: VDX; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3cv9.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
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