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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 318 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 280 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 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 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 8BO 0.462963 0.822222
25 9RO 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: 110
This union binding pocket(no: 1) in the query (biounit: 3a51.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 1ZEI CRS None
3 3OCP CMP None
4 1UO5 PIH None
5 1UO4 PIH None
6 1V8B ADN 1.21654
7 3ZVS MLI 1.875
8 3OJF NDP 1.94553
9 4TV1 36M 1.99203
10 5CX8 TG6 2.18978
11 4OKZ 3E9 2.19178
12 5XSJ XYP 2.28758
13 5ZM0 FAD 2.43309
14 5IM3 DTP 2.43309
15 1RL4 BL5 2.65957
16 4DDY DN6 2.6616
17 6AZQ C5J 2.67176
18 4GU5 FAD 2.6764
19 5OSW DIU 2.91971
20 3BJC WAN 2.91971
21 4WGF HX2 2.92683
22 5F1R 42O 2.95359
23 1PZO CBT 3.04183
24 2JFZ DGL 3.13725
25 2X1L MET 3.16302
26 3RV5 DXC 3.37079
27 5LX9 OLB 3.58306
28 4DW4 U5P 3.59281
29 2OWZ CIT 3.61446
30 4MRP GSH 3.64964
31 3HYW DCQ 3.64964
32 1NP7 FAD 3.64964
33 5Y02 HBX 3.73832
34 5Y02 MXN 3.73832
35 4OHU NAD 3.80623
36 4OHU 2TK 3.80623
37 1XX4 BAM 3.83142
38 5ESO ISC 3.89294
39 5ESO TDP 3.89294
40 2QV6 GTP 4.10448
41 3LE7 ADE 4.21456
42 5EEH P9P 4.25532
43 3VRV YSD 4.42804
44 5UWA 8ND 4.4335
45 3GZ9 D32 4.46097
46 4RW3 TDA 4.63576
47 2E3N 6CM 4.70588
48 4URX FK1 4.86486
49 4O4Z N2O 5.19481
50 6BVM EBV 5.38922
51 6D5H FV7 5.38922
52 6D56 FVM 5.38922
53 6BVK EAV 5.38922
54 6D59 FVJ 5.38922
55 6BVJ EAS 5.38922
56 6D55 FWA 5.38922
57 6D5G FVD 5.38922
58 6BVL EBY 5.38922
59 6BVI EC4 5.38922
60 5OC1 ANN 6.32603
61 1A05 IPM 6.70391
62 5OLK DTP 6.81265
63 1Y4Z PCI 7.11111
64 2R2N KYN 7.29927
65 5LWY OLB 7.47664
66 3WFD AXO 8.21918
67 4OIC A8S 8.75912
68 3KP6 SAL 9.27152
69 3V1S 0LH 9.62733
70 1MID LAP 10.989
71 3NJQ NJQ 11.399
72 3VVY ET 11.8557
73 2Z6D FMN 12.3077
74 2YLD CMO 12.5984
75 2FDW D3G 13.8686
76 5HCN DAO 14.1762
77 3G4Q MCH 16.4384
78 3T3Z 9PL 16.545
79 4XRZ SI6 16.7883
80 3MDV CL6 18.7348
81 4F4S EFO 19.7368
82 4NKW PLO 20.438
83 2QQD AG2 20.7547
84 2HI4 BHF 21.1679
85 1ZOA 140 22.3844
86 1MT1 AG2 23.0769
87 4QXB OGA 23.5294
88 5ZCO PGV 23.913
89 5ZCO CHD 23.913
90 5Z84 PGV 23.913
91 5Z84 CHD 23.913
92 4V1F BQ1 24.4186
93 1N6B DMZ 25.0608
94 6CR2 LFV 27.0073
95 5D48 L96 28.9474
96 4RQL SNE 32.1168
97 4OGQ 1O2 32.4324
98 3LXI CAM 36.253
99 5K7K 6RJ 38.4428
100 1RE9 DSO 40.146
101 4JX1 CAM 40.146
102 4JX1 CAH 40.146
103 4L77 CNL 40.7035
104 5D3U TRP 43.7956
105 5IBE 69M 44.697
106 2X5W K2B 45.4988
107 2XFH CL6 47.2019
108 2WH8 II2 48.4185
109 3ABA FLI 49.3917
110 6BLD DXJ 49.3917
111 5L92 C0R 50
112 5L92 MLA 50
Pocket No.: 2; Query (leader) PDB : 3A51; Ligand: VDY; Similar sites found with APoc: 32
This union binding pocket(no: 2) in the query (biounit: 3a51.bio3) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 1NU4 MLA None
2 1NE7 16G 1.7301
3 1Y7I SAL 1.86567
4 1M3U KPL 1.89394
5 3ZQE DXC 1.96721
6 4O08 PO6 2.49221
7 1L0I PSR 2.5641
8 3CEV ARG 2.67559
9 2XXP DSL 2.76382
10 2FZW NAD 2.94906
11 1J78 OLA 3.16302
12 3WUR O4B 3.50877
13 3GQT UFO 3.50877
14 6CB2 OLC 3.75427
15 5FH7 5XL 4.03226
16 5EZ1 ICB 4.33213
17 4D4U FUC NDG GAL FUC 4.37956
18 4J7Q B7N 4.5045
19 1U3D FAD 4.62287
20 5X3R 7Y3 4.87805
21 5TVI MYR 5.43478
22 3KFC 61X 5.5336
23 5XK9 GST 5.60345
24 5NM7 GLY 5.6391
25 1JGS SAL 5.7971
26 2J1P GRG 6.48464
27 1XZ3 ICF 8.04598
28 6CEP OXM 8.68263
29 2Y69 CHD 15.7143
30 5W97 CHD 23.913
31 4XU6 TDA 27.1429
32 2VE3 REA 29.4404
Pocket No.: 3; Query (leader) PDB : 3A51; Ligand: VDY; Similar sites found with APoc: 16
This union binding pocket(no: 3) in the query (biounit: 3a51.bio5) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 4PSB GA3 None
2 3NY4 SMX 2.64151
3 5ICE 2H4 2.84091
4 1YKD CMP 3.01508
5 4E70 N7I 3.35052
6 1TMO 2MD 3.40633
7 2AX9 BHM 3.51562
8 5UR6 8KM 3.8674
9 5JO1 6LM 4.47761
10 2EQA AMP 6.53409
11 3HAV ATP 6.68896
12 1W2Y DUN 6.9869
13 3NB0 G6P 7.29927
14 3SFI 3SF 8.8983
15 2QZT PLM 9.90991
16 2GBB CIT 12.1795
Pocket No.: 4; Query (leader) PDB : 3A51; Ligand: VDY; Similar sites found with APoc: 17
This union binding pocket(no: 4) in the query (biounit: 3a51.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 2I7C AAT 2.4735
2 4Z3E GAL NGA GLA BGC GAL 2.52525
3 3QIN P1Y 2.66667
4 3WYJ H78 3.16302
5 1XSE NDP 3.38983
6 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 4.08163
7 3WCA FPS 4.13625
8 5DKK FMN 4.13793
9 4XT8 TMQ 4.26357
10 4RW3 PLM 4.63576
11 4WAS NAP 4.67033
12 5B0I BOG 5.59611
13 3OIG NAD 5.6391
14 5ML3 DL3 6.04027
15 6GG9 FMN 8.02469
16 1Q7E MET 8.41121
17 2DYR PGV 23.913
Pocket No.: 5; Query (leader) PDB : 3A51; Ligand: VDY; Similar sites found with APoc: 40
This union binding pocket(no: 5) in the query (biounit: 3a51.bio4) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 5M67 ADE 1.94647
2 5M67 NAD 1.94647
3 1Q9I TEO 2.18978
4 1Q9I FAD 2.18978
5 2H7C COA 2.21402
6 3V66 D3A 2.35294
7 3EBL GA4 2.46575
8 4KWD JF2 2.54777
9 4C2X NHW 3.17073
10 2YNC YNC 3.38542
11 4HIA FMN 3.40909
12 5E7V M7E 4
13 5T2Z 017 4.0404
14 1LDN NAD 4.11392
15 5CFQ 1SY 4.27807
16 5DEY 59T 4.3771
17 3ET3 ET1 4.45205
18 5MN0 A8S 4.5045
19 4HEE 14R 4.60993
20 3KMR EQN 4.88722
21 5K13 6Q7 5.28455
22 5XK9 DMA 5.60345
23 4WT2 3UD 5.71429
24 4YBN FAD 5.80357
25 4QGE 35O 6.56934
26 2WKQ FMN 6.62651
27 4M8E 29V 6.92641
28 5SVV FMN 8.0292
29 2V0U FMN 8.21918
30 5EFW FMN 8.33333
31 3T50 FMN 8.59375
32 2PR5 FMN 9.09091
33 2ZSH GA3 9.09091
34 1FDQ HXA 9.16031
35 1M2Z BOG 9.72763
36 6GBV FMN 10.274
37 3IPQ 965 10.9489
38 5JNN 6LM 11.5789
39 3FAL LO2 16.9173
40 4OIV XX9 28.7611
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