Receptor
PDB id Resolution Class Description Source Keywords
3A51 2 Å EC: 1.-.-.- STRUCTURE OF CYTOCHROME P450 VDH MUTANT (VDH-K1) OBTAINED BY EVOLUTION WITH BOUND 25-HYDROXYVITAMIN D3 PSEUDONOCARDIA AUTOTROPHICA CYTOCHROME P450 VITAMIN D3 HYDROXYLASE HEMOPROTEIN MONOOXDIRECTED EVOLUTION OXIDOREDUCTASE
Ref.: STRUCTURAL EVIDENCE FOR ENHANCEMENT OF SEQUENTIAL V HYDROXYLATION ACTIVITIES BY DIRECTED EVOLUTION OF C P450 VITAMIN D3 HYDROXYLASE J.BIOL.CHEM. V. 285 31193 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT A:4006;
B:4009;
C:4004;
C:4007;
D:4001;
E:4005;
E:4008;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
59.044 C2 H3 O2 CC(=O...
CA A:2501;
A:2505;
A:2506;
C:2503;
D:2502;
E:2504;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
GOL A:3001;
A:3002;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
HEM A:412;
B:412;
C:412;
D:412;
E:412;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
submit data
616.487 C34 H32 Fe N4 O4 Cc1c2...
VDY A:6178;
B:6178;
C:6178;
D:6178;
E:6178;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
submit data
400.637 C27 H44 O2 C[C@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3A51 2 Å EC: 1.-.-.- STRUCTURE OF CYTOCHROME P450 VDH MUTANT (VDH-K1) OBTAINED BY EVOLUTION WITH BOUND 25-HYDROXYVITAMIN D3 PSEUDONOCARDIA AUTOTROPHICA CYTOCHROME P450 VITAMIN D3 HYDROXYLASE HEMOPROTEIN MONOOXDIRECTED EVOLUTION OXIDOREDUCTASE
Ref.: STRUCTURAL EVIDENCE FOR ENHANCEMENT OF SEQUENTIAL V HYDROXYLATION ACTIVITIES BY DIRECTED EVOLUTION OF C P450 VITAMIN D3 HYDROXYLASE J.BIOL.CHEM. V. 285 31193 2010
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 352 families.
1 3A50 - VD3 C27 H44 O CC(C)CCC[C....
2 3A51 - VDY C27 H44 O2 C[C@H](CCC....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 311 families.
1 3A50 - VD3 C27 H44 O CC(C)CCC[C....
2 3A51 - VDY C27 H44 O2 C[C@H](CCC....
50% Homology Family (46)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 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 4J6C - STR C21 H30 O2 CC(=O)[C@H....
6 4JBT - ASD C19 H26 O2 C[C@]12CCC....
7 4J6B - PLO C21 H32 O2 CC(=O)[C@H....
8 4J6D - TES C19 H28 O2 C[C@]12CC[....
9 5XJN - 88L C8 H11 O4 P CCc1ccc(cc....
10 4UBS Kd = 65 uM DIF C14 H11 Cl2 N O2 c1ccc(c(c1....
11 5L1O Kd = 7.2 uM 7PF C15 H18 O5 CC1(C[C@H]....
12 5L1U Kd = 340 uM 7PF C15 H18 O5 CC1(C[C@H]....
13 5L1S Kd = 160 uM 7PF C15 H18 O5 CC1(C[C@H]....
14 5L1V Kd = 43 uM 7PF C15 H18 O5 CC1(C[C@H]....
15 5L1Q Kd = 170 uM 7DF C15 H20 O5 CC1(C[C@H]....
16 5L1P - 7PT C15 H16 O5 C[C@H]1[C@....
17 2NZ5 Kd = 10.5 uM 226 C10 H8 O5 c1c(cc(c2c....
18 5IT1 - 2OH C15 H16 O2 CC(C)(c1cc....
19 2WI9 Kd = 309 uM 1D2 C20 H39 N O3 C[C@@H]1C[....
20 2VZM Kd = 171.9 uM NRB C28 H47 N O7 CC[C@@H]1[....
21 4B7S Kd = 81 uM QLE C22 H37 N O5 CC[C@@H]1[....
22 3ZK5 Kd = 118 uM Z18 C21 H35 N O5 CC[C@@H]1[....
23 5X7E - 7ZU C28 H44 O3 C[C@H](/C=....
24 2ZBZ - VDX C27 H44 O3 C[C@H](CCC....
25 3CV9 - VDX C27 H44 O3 C[C@H](CCC....
26 2XBK Kd = 4 uM XBK C33 H47 N O12 C[C@@H]1CC....
27 1Z8Q - DEB C21 H38 O6 CC[C@@H]1[....
28 1Z8P - DEB C21 H38 O6 CC[C@@H]1[....
29 1JIN - KTN C26 H28 Cl2 N4 O4 CC(=O)N1CC....
30 1JIO - DEB C21 H38 O6 CC[C@@H]1[....
31 1Z8O - DEB C21 H38 O6 CC[C@@H]1[....
32 2D09 Kd = 7.3 uM FLV C10 H6 O5 c1c(cc(c2c....
33 1T93 - FLV C10 H6 O5 c1c(cc(c2c....
34 2D0E Kd = 43 uM NQ C10 H6 O3 c1ccc2c(c1....
35 1XQD Kd = 0.07 mM DND C21 H27 N6 O15 P2 c1cc(c[n+]....
36 6GK6 Kd = 2.1 uM MYR C14 H28 O2 CCCCCCCCCC....
37 5L91 Kd = 91 uM C0R C21 H30 O4 C[C@]12CCC....
38 5L94 Kd = 105 uM TES C19 H28 O2 C[C@]12CC[....
39 4AW3 - MYV C37 H61 N O12 CC[C@@H]1[....
40 2Y5N - MYV C37 H61 N O12 CC[C@@H]1[....
41 3ZSN - MIV C37 H61 N O11 CC[C@@H]1[....
42 2Y98 - MIV C37 H61 N O11 CC[C@@H]1[....
43 2Y5Z - ZM3 C36 H59 N O11 CC[C@@H]1[....
44 2YCA - ZM3 C36 H59 N O11 CC[C@@H]1[....
45 2Y46 - MIV C37 H61 N O11 CC[C@@H]1[....
46 3WVS - RRM C32 H48 O7 CCCC[C@H]1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: VDY; Similar ligands found: 40
No: Ligand ECFP6 Tc MDL keys Tc
1 VDY 1 1
2 VD3 0.78481 0.921053
3 VDX 0.712644 0.926829
4 VDZ 0.694118 0.926829
5 YSV 0.694118 0.926829
6 MVD 0.677778 0.926829
7 VD2 0.674419 0.902439
8 C33 0.642105 0.904762
9 O1C 0.635417 0.863636
10 C3O 0.628866 0.826087
11 OCC 0.616162 0.808511
12 AYT 0.582418 1
13 YS3 0.566667 0.902439
14 YS2 0.555556 0.840909
15 BIV 0.541667 0.926829
16 AKX 0.528846 0.860465
17 B0B 0.520833 1
18 YSD 0.515789 0.857143
19 AYK 0.5 0.72549
20 M7E 0.490741 0.649123
21 TX5 0.475248 0.880952
22 VD1 0.472527 0.878049
23 ZNE 0.464286 0.698113
24 9RO 0.462963 0.822222
25 8BO 0.462963 0.822222
26 H97 0.457944 0.787234
27 G72 0.457944 0.787234
28 8BL 0.453704 0.840909
29 TEJ 0.443396 0.782609
30 YA1 0.442308 0.904762
31 7ZU 0.431373 0.878049
32 JC1 0.424528 0.822222
33 8J0 0.419643 0.837209
34 8J3 0.419643 0.837209
35 YI3 0.419048 0.880952
36 KH1 0.418182 0.822222
37 MC9 0.417476 0.833333
38 91W 0.415094 0.8
39 YI4 0.411215 0.840909
40 EB1 0.409091 0.857143
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3A51; Ligand: VDY; 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: 3a51.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 5L92 C0R 50
Pocket No.: 2; Query (leader) PDB : 3A51; Ligand: VDY; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3a51.bio3) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 5L92 C0R 50
Pocket No.: 3; Query (leader) PDB : 3A51; Ligand: VDY; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3a51.bio5) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 5L92 C0R 50
Pocket No.: 4; Query (leader) PDB : 3A51; Ligand: VDY; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 3a51.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 5L92 C0R 50
Pocket No.: 5; Query (leader) PDB : 3A51; Ligand: VDY; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 3a51.bio4) has 17 residues
No: Leader PDB Ligand Sequence Similarity
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