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 280 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 247 families.
1 3A50 - VD3 C27 H44 O CC(C)CCC[C....
2 3A51 - VDY C27 H44 O2 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: VDY; Similar ligands found: 32
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 YS3 0.566667 0.902439
13 YS2 0.555556 0.840909
14 BIV 0.541667 0.926829
15 AKX 0.528846 0.860465
16 YSD 0.515789 0.857143
17 M7E 0.490741 0.649123
18 TX5 0.475248 0.880952
19 VD1 0.472527 0.878049
20 ZNE 0.464286 0.698113
21 H97 0.457944 0.787234
22 G72 0.457944 0.787234
23 TEJ 0.443396 0.782609
24 YA1 0.442308 0.904762
25 7ZU 0.431373 0.878049
26 JC1 0.424528 0.822222
27 YI3 0.419048 0.880952
28 KH1 0.418182 0.822222
29 MC9 0.417476 0.833333
30 91W 0.415094 0.8
31 YI4 0.411215 0.840909
32 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: 40
This union binding pocket(no: 1) in the query (biounit: 3a51.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3OCP CMP 0.01172 0.40465 None
2 1UO5 PIH 0.009706 0.40416 None
3 1UO4 PIH 0.03102 0.40065 None
4 3OJF NDP 0.01773 0.40937 1.94553
5 5CX8 TG6 0.01595 0.40755 2.18978
6 4OKZ 3E9 0.007225 0.41195 2.19178
7 1RL4 BL5 0.01807 0.40529 2.65957
8 2JFZ DGL 0.03354 0.41254 3.13725
9 2X1L MET 0.01143 0.41621 3.16302
10 4MRP GSH 0.009162 0.42811 3.64964
11 3HYW DCQ 0.01103 0.41022 3.64964
12 1NP7 FAD 0.01868 0.40014 3.64964
13 1XX4 BAM 0.001723 0.48034 3.83142
14 3LE7 ADE 0.01894 0.40221 4.21456
15 4RW3 TDA 0.04054 0.40236 4.63576
16 2R2N KYN 0.01142 0.40995 7.29927
17 2Q8H TF4 0.005253 0.4265 7.54258
18 3WFD AXO 0.03196 0.40054 8.21918
19 4OIC A8S 0.007314 0.40236 8.75912
20 3V1S 0LH 0.006822 0.4243 9.62733
21 2YLD CMO 0.0103 0.4187 12.5984
22 2FDW D3G 0.004114 0.43122 13.8686
23 5HCN DAO 0.02105 0.40064 14.1762
24 4XRZ SI6 0.0008501 0.41661 16.7883
25 3MDV CL6 0.006891 0.41139 18.7348
26 4NKW PLO 0.007758 0.40123 20.438
27 2QQD AG2 0.0107 0.41549 20.7547
28 2HI4 BHF 0.001837 0.42338 21.1679
29 1ZOA 140 0.01983 0.40805 22.3844
30 1MT1 AG2 0.00838 0.42085 23.0769
31 1N6B DMZ 0.002857 0.42048 25.0608
32 2VE3 REA 0.00447 0.42465 29.4404
33 4RQL SNE 0.004096 0.43131 32.1168
34 3LXI CAM 0.0003563 0.49337 36.253
35 1RE9 DSO 0.002184 0.44077 40.146
36 5D3U TRP 0.0018 0.45444 43.7956
37 2X5W K2B 0.00000808 0.46553 45.4988
38 5GWE GWM 0.009091 0.41434 46.4198
39 5XJN 88L 0.0007844 0.45526 47.2019
40 2WH8 II2 0.0006738 0.46963 48.4185
Pocket No.: 2; Query (leader) PDB : 3A51; Ligand: VDY; Similar sites found: 6
This union binding pocket(no: 2) in the query (biounit: 3a51.bio3) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1L0I PSR 0.01835 0.40252 2.5641
2 3GQT UFO 0.01204 0.40207 3.50877
3 4D4U FUC NDG GAL FUC 0.02219 0.40214 4.37956
4 4J7Q B7N 0.01063 0.41555 4.5045
5 1JGS SAL 0.01554 0.41847 5.7971
6 1XZ3 ICF 0.02694 0.41568 8.04598
Pocket No.: 3; Query (leader) PDB : 3A51; Ligand: VDY; Similar sites found: 5
This union binding pocket(no: 3) in the query (biounit: 3a51.bio5) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WG0 CHD 0.0181 0.41158 None
2 4PSB GA3 0.02469 0.40028 None
3 3KDU NKS 0.03261 0.40618 3.97112
4 5JO1 6LM 0.00919 0.40373 4.47761
5 2QZT PLM 0.009812 0.41329 9.90991
Pocket No.: 4; Query (leader) PDB : 3A51; Ligand: VDY; Similar sites found: 7
This union binding pocket(no: 4) in the query (biounit: 3a51.bio2) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1M3U KPL 0.01724 0.40068 1.89394
2 2PT9 2MH 0.02229 0.40351 2.18069
3 4Z3E GAL NGA GLA BGC GAL 0.01959 0.40111 2.52525
4 3QIN P1Y 0.0147 0.40277 2.66667
5 3WCA FPS 0.0161 0.40184 4.13625
6 4RW3 PLM 0.03992 0.40313 4.63576
7 1W2Y DUN 0.008633 0.40672 6.9869
Pocket No.: 5; Query (leader) PDB : 3A51; Ligand: VDY; Similar sites found: 6
This union binding pocket(no: 5) in the query (biounit: 3a51.bio4) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3EBL GA4 0.01417 0.40409 2.46575
2 4C2X NHW 0.04152 0.40132 3.17073
3 2YNC YNC 0.03085 0.40415 3.38542
4 5E7V M7E 0.0197 0.4072 4
5 1FDQ HXA 0.02511 0.40073 9.16031
6 5JNN 6LM 0.01634 0.4043 11.5789
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