Receptor
PDB id Resolution Class Description Source Keywords
5X7E 1.9 Å EC: 1.14.14.1 CRYSTAL STRUCTURE OF VITAMIN D HYDROXYLASE CYTOCHROME P450 1 MUTANT) IN COMPLEX WITH 1,25-DIHYDROXYVITAMIN D2 STREPTOMYCES GRISEOLUS METAL-BINDING MONOOXYGENASE OXIDOREDUCTASE
Ref.: PRODUCTION OF AN ACTIVE FORM OF VITAMIN D2 BY GENET ENGINEERED CYP105A1 BIOCHEM. BIOPHYS. RES. V. 486 336 2017 COMMUN.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
HEM A:501;
Part of Protein;
none;
submit data
616.487 C34 H32 Fe N4 O4 Cc1c2...
7ZU A:502;
Valid;
none;
submit data
428.647 C28 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: 1.14.14.1 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 9 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 5 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 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: 7ZU; Similar ligands found: 36
No: Ligand ECFP6 Tc MDL keys Tc
1 7ZU 1 1
2 MC9 0.761905 0.95
3 EB1 0.706522 0.926829
4 VDX 0.641304 0.951219
5 BIV 0.630435 0.951219
6 TX5 0.623656 0.951219
7 91W 0.617021 0.906977
8 FMV 0.614583 0.866667
9 KH1 0.59596 0.844444
10 JC1 0.59375 0.844444
11 TEJ 0.565657 0.844444
12 6VH 0.553398 0.829787
13 ICJ 0.543689 0.928571
14 M7E 0.523364 0.637931
15 ZNE 0.509091 0.716981
16 COV 0.485437 0.847826
17 0CO 0.485437 0.847826
18 NYA 0.470588 0.95
19 VDP 0.459677 0.603175
20 MVD 0.443396 0.951219
21 ZYD 0.431373 0.951219
22 VDY 0.431373 0.878049
23 MI4 0.428571 0.926829
24 TT2 0.423423 0.926829
25 O1C 0.419643 0.886364
26 YS3 0.415842 0.975
27 C33 0.410714 0.928571
28 OCC 0.408696 0.829787
29 YS2 0.405941 0.863636
30 VDZ 0.403846 0.951219
31 YSD 0.403846 0.926829
32 YSV 0.403846 0.951219
33 C3O 0.403509 0.847826
34 VHW 0.403226 0.730769
35 VD1 0.402062 0.902439
36 VD3 0.401961 0.804878
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3CV9; Ligand: VDX; Similar sites found: 21
This union binding pocket(no: 1) in the query (biounit: 3cv9.bio1) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3X01 AMP 0.04797 0.40042 1.78117
2 4HXY ACA 0.02788 0.41005 2.18447
3 3HP9 CF1 0.01766 0.42166 2.42718
4 3V78 ET 0.01496 0.41312 2.88462
5 3K8D CTP 0.01996 0.40339 2.91262
6 2HK9 ATR 0.01427 0.41805 3.63636
7 4MRP GSH 0.00471 0.44857 3.64078
8 3WBG 2AN 0.01951 0.40052 3.92157
9 1TZD ADP 0.01811 0.42885 4
10 4MC3 28U 0.03336 0.40698 4.62428
11 1TW4 CHD 0.01645 0.41108 4.8
12 2WPB ZZI 0.02565 0.4131 5.59211
13 2Y6P CTP 0.01601 0.40802 5.98291
14 1FLJ GSH 0.02264 0.41551 6.53846
15 4O4Z N2O 0.02354 0.40797 7.14286
16 4OSP 2V4 0.01285 0.42909 7.98479
17 4MGA 27L 0.02501 0.41403 9.01961
18 3E81 SLB 0.02326 0.41686 20.122
19 2YOO K2B 0.0008034 0.45679 40.0491
20 4DO1 ANN 0.005781 0.45496 40.7317
21 2WM4 VGJ 0.005657 0.42216 41.7476
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