Receptor
PDB id Resolution Class Description Source Keywords
5GID 2.15 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF VDR IN COMPLEX WITH DLAM-4 (C2 FORM) RATTUS NORVEGICUS NUCLEAR RECEPTOR TRANSCRIPTION
Ref.: REGULATION OF THE VITAMIN D RECEPTOR BY VITAMIN D L DERIVATIVES. FEBS LETT. V. 590 3270 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ASN HIS PRO MET LEU MET ASN LEU LEU C:626;
Invalid;
none;
submit data n/a n/a n/a n/a
VDP A:501;
Valid;
none;
Kd = 769.2 nM
575.821 C37 H53 N O4 C[C@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5GIC 2.35 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF VDR IN COMPLEX WITH DLAM-2P RATTUS NORVEGICUS NUCLEAR RECEPTOR TRANSCRIPTION
Ref.: REGULATION OF THE VITAMIN D RECEPTOR BY VITAMIN D L DERIVATIVES. FEBS LETT. V. 590 3270 2016
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 263 families.
1 5GIE Kd = 769.2 nM VDP C37 H53 N O4 C[C@H](C[C....
2 5GID Kd = 769.2 nM VDP C37 H53 N O4 C[C@H](C[C....
3 5GIC Kd = 330.9 nM DLC C35 H51 N O4 C[C@H]1/C(....
70% Homology Family (30)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 222 families.
1 4Q0A Kd = 0.33 uM 4OA C24 H40 O3 C[C@H](CCC....
2 3A3Z - 2MV C29 H46 O4 C[C@H]1[C@....
3 1IE8 - KH1 C29 H48 O4 CCC(CC)(CC....
4 2HAS - C3O C30 H50 O4 CCCO[C@H]1....
5 1S0Z - EB1 C30 H46 O3 CCC(CC)(C=....
6 3AZ1 - DS2 C27 H38 O5 CCC(CC)(c1....
7 1IE9 - VDX C27 H44 O3 C[C@H](CCC....
8 2HAM - C33 C30 H50 O3 CCC[C@H]1[....
9 2HB8 - MVD C28 H46 O3 C[C@H]1[C@....
10 3CS4 - COV C28 H44 O4 C[C@]12CCC....
11 1S19 - MC9 C27 H40 O3 C[C@H](C=C....
12 3M7R - VDX C27 H44 O3 C[C@H](CCC....
13 3A40 - 23R C29 H46 O4 C[C@H]1[C@....
14 3AUR - CA9 C27 H42 O3 C[C@H]1[C@....
15 3KPZ - ZNE C28 H41 N O3 S C[C@H](CCC....
16 1TXI - TX5 C27 H40 O3 C[C@H](CC#....
17 1DB1 Kd = 0.55 nM VDX C27 H44 O3 C[C@H](CCC....
18 4G2I - 0VQ C25 H26 F6 O3 CC/C(=CC=C....
19 3CS6 - 0CO C28 H44 O4 C[C@]12CCC....
20 3AZ2 - DS3 C30 H44 O5 CCC(CC)(c1....
21 3AZ3 - DS6 C31 H46 O5 CCC(CC)(c1....
22 2HB7 - O1C C30 H50 O4 C[C@H](CCC....
23 3VHW - VHW C34 H50 O7 CCC1(CC/C(....
24 2HAR - OCC C30 H50 O5 C[C@H](CCC....
25 3TKC - FMV C28 H40 O4 C[C@H](c1c....
26 4ITE - TEY C30 H48 N4 O3 C[C@H](CCC....
27 3P8X - ZYD C27 H44 O3 CC(C)(CCCC....
28 5GIE Kd = 769.2 nM VDP C37 H53 N O4 C[C@H](C[C....
29 5GID Kd = 769.2 nM VDP C37 H53 N O4 C[C@H](C[C....
30 5GIC Kd = 330.9 nM DLC C35 H51 N O4 C[C@H]1/C(....
50% Homology Family (131)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 185 families.
1 3ILZ - B72 C20 H24 O4 Cc1cc(cc(c....
2 3HZF - B72 C20 H24 O4 Cc1cc(cc(c....
3 1NAV - IH5 C17 H16 Cl2 O4 CC(C)c1cc(....
4 4LNX - T44 C15 H11 I4 N O4 c1c(cc(c(c....
5 2H77 - T3 C15 H12 I3 N O4 c1cc(c(cc1....
6 2Q61 - SF1 C22 H16 Cl N O2 S c1ccc(cc1)....
7 3AN3 - M7S C37 H43 N O4 CCCOc1ccc(....
8 1ZEO ic50 = 0.21 uM C01 C25 H30 N O5 CCCc1cc2c(....
9 3R8I Kd = 4.5 uM XCX C26 H34 N2 O4 CCCCCCCN(C....
10 3ADW Kd = 72.8 uM MYI C11 H11 N O3 COc1ccc2c(....
11 4E4K - RRG C24 H24 O3 CC(C)c1ccc....
12 4XUH ic50 = 1.87 uM SFI C20 H17 F O2 S CC1=C(c2cc....
13 2POB - GW4 C36 H35 N3 O4 Cc1c(nc(o1....
14 2HWR - DRD C35 H35 N O5 CCCc1c2ccc....
15 4R2U - 3JX C33 H29 N3 O5 Cc1c(n(c2c....
16 2ZNO - S44 C32 H41 N O4 CCCOc1ccc(....
17 4XUM ic50 = 21.3 uM IMN C19 H16 Cl N O4 Cc1c(c2cc(....
18 3R5N Kd = 1.67 uM MLO C18 H18 O2 C=CCc1ccc(....
19 2HWQ - DRY C33 H31 N O5 CCCc1c2ccc....
20 3VJH - J35 C22 H24 F3 N O4 CCC[C@@H](....
21 3U9Q Ki = 41.7 uM DKA C10 H20 O2 CCCCCCCCCC....
22 2Q6R - SF2 C23 H18 Cl N O3 S COc1cccc(c....
23 2P4Y Ki = 0.001 uM C03 C28 H22 Cl F3 N2 O6 Cc1c(c2ccc....
24 3D6D - LRG C21 H18 O3 c1ccc(cc1)....
25 2F4B ic50 = 50 nM EHA C33 H31 N O5 CCCc1c2ccc....
26 3BC5 ic50 = 0.005 uM ZAA C29 H26 N4 O4 Cc1c(nc(o1....
27 3VSO - EK1 C31 H31 N3 O4 CCCOc1ccc(....
28 4R06 Kd = 565 nM 3E7 C28 H24 N2 O3 S CC[C@@H](c....
29 1I7I - AZ2 C20 H24 O7 S CCO[C@@H](....
30 4R6S - 3K2 C33 H29 N3 O5 Cc1c(n(c2c....
31 3GBK - 2PQ C38 H41 N O5 CCCc1cc(cc....
32 3SZ1 - LU2 C15 H10 O6 c1cc(c(cc1....
33 2ZVT - PTG C20 H28 O3 CCCCCC=CC=....
34 2ATH ic50 = 0.152 uM 3EA C24 H23 F3 N2 O5 CCCc1c(ccc....
35 4XLD - BRL C18 H19 N3 O3 S CN(CCOc1cc....
36 2G0H ic50 = 22.7 nM SP3 C21 H12 F7 N3 O2 S2 c1cc(sc1)c....
37 2Q5P - 241 C28 H24 F3 N O6 Cc1c(c2cc(....
38 2GTK ic50 = 0.251 uM 208 C24 H23 Cl N2 O4 CCO[C@@H](....
39 4Y29 ic50 = 566 nM CTI C21 H18 N O4 C[n+]1cc2c....
40 2I4J - DRJ C27 H36 N2 O4 CCCCCCCN(C....
41 3R8A - HIG C26 H25 N7 CCc1nc2c(c....
42 4XTA ic50 = 3.7 uM DIF C14 H11 Cl2 N O2 c1ccc(c(c1....
43 3TY0 ic50 = 83.1 nM 082 C26 H20 N4 O6 C[C@]1(C(=....
44 4YT1 - JJB C29 H28 N4 O5 S CCCOc1ccc(....
45 2ZK6 - C08 C22 H31 B F2 N2 O2 [B-]1(n2c(....
46 3ADS Kd = 9.73 uM IMN C19 H16 Cl N O4 Cc1c(c2cc(....
47 3ET0 - GLC C6 H12 O6 C([C@@H]1[....
48 4E4Q - RRH C24 H24 O3 CC(C)c1ccc....
49 1KNU - YPA C25 H25 N O4 CCO[C@@H](....
50 2Q8S ic50 = 0.185 uM L92 C26 H26 N2 O3 Cc1c(nc(o1....
51 2YFE Ki = 0.236 uM YFE C21 H24 O4 CC(=CCc1c(....
52 4EM9 - KNA C9 H18 O2 CCCCCCCCC(....
53 2Q6S - PLB C18 H11 Cl2 N3 O4 c1cnc(nc1)....
54 3AN4 - M7R C37 H43 N O4 CCCOc1ccc(....
55 3PBA - ZXG C15 H12 Br4 O5 S CC(C)(c1cc....
56 3ADV Kd = 933 uM SRO C10 H12 N2 O c1cc2c(cc1....
57 2Q5S - NZA C22 H15 Cl2 N O2 S c1ccc(cc1)....
58 5F9B - 5VN C30 H48 O5 C[C@]12CC[....
59 2I4P - DRH C27 H36 N2 O4 CCCCCCC[N@....
60 5LSG Kd = 4 uM QZQ C30 H46 O3 CC(=C)[C@@....
61 5TTO - 7KK C21 H11 Br Cl2 F2 N2 O3 S c1ccc2c(c1....
62 5HZC - 65W C20 H18 O3 CC(C)(C(=O....
63 3IA6 ic50 = 0.003 uM UNT C24 H24 N4 O3 Cc1c(nc(o1....
64 3ADX - IMN C19 H16 Cl N O4 Cc1c(c2cc(....
65 3HOD - ZZH C22 H20 O3 c1ccc(cc1)....
66 2I4Z - DRH C27 H36 N2 O4 CCCCCCC[N@....
67 2AWH - VCA C18 H34 O2 CCCCCCC=CC....
68 5U3Y - 7U7 C27 H29 N O5 c1ccc(c(c1....
69 5U3T - 7UY C27 H31 N O4 S CC(C)N(Cc1....
70 5U3X - 7U4 C28 H30 N2 O4 c1ccc(c(c1....
71 2BAW - VCA C18 H34 O2 CCCCCCC=CC....
72 5U3Z - 7UA C27 H29 N O5 c1ccc(c(c1....
73 5U3Q - 7UJ C29 H33 N O4 CC(C)N(Cc1....
74 5U45 - 7SY C29 H30 F N O4 c1ccc(c(c1....
75 3SP9 - IL2 C22 H32 O4 CC#CC[C@@H....
76 3GWX ic50 = 4 uM EPA C20 H30 O2 CCC=C/CC=C....
77 5U3V - 7TY C29 H33 N O5 c1ccc(c(c1....
78 2XYJ - WLM C21 H23 Cl N4 O4 S2 CC(C)c1nnc....
79 5U3S - 7V4 C27 H31 N O5 CC(C)N(Cc1....
80 5U3W - 7U1 C29 H31 N O4 c1ccc(cc1)....
81 5U40 - 7UD C31 H31 N O5 c1ccc(cc1)....
82 1GWX - 433 C28 H28 Cl3 F N2 O4 CC(C)(C(=O....
83 5U44 - 7SV C29 H30 F N O4 c1ccc(c(c1....
84 3TKM Kd = 22 nM GW0 C21 H17 F4 N O3 S2 Cc1cc(ccc1....
85 5U41 - 7UG C31 H31 N O4 S c1ccc(cc1)....
86 5U42 - 7SM C30 H33 N O5 COc1cccc(c....
87 5U3U - 7TV C29 H33 N O5 c1ccc(c(c1....
88 3GZ9 Ki = 0.004 uM D32 C27 H23 F3 O5 S Cc1c(c(ccc....
89 5U46 - 7T1 C21 H18 F3 N O3 S2 Cc1cc(ccc1....
90 5U3R - 7V1 C27 H31 N O5 CC(C)N(Cc1....
91 3ET2 - ET1 C19 H19 N O6 S COc1ccc(cc....
92 5U43 - 7SS C30 H33 N O5 COc1ccc(cc....
93 2B50 - VCA C18 H34 O2 CCCCCCC=CC....
94 3PEQ ic50 = 32 nM 3EQ C30 H31 N O5 S2 CCCC[N@@](....
95 4BCR - WY1 C14 H14 Cl N3 O2 S Cc1cccc(c1....
96 1I7G ic50 = 1 uM AZ2 C20 H24 O7 S CCO[C@@H](....
97 3KDU ic50 = 347 nM NKS C28 H25 Cl N2 O6 Cc1ccc(cc1....
98 3VI8 - 13M C30 H27 N O4 CC[C@@H](C....
99 2ZNN - S44 C32 H41 N O4 CCCOc1ccc(....
100 5HYK - 65W C20 H18 O3 CC(C)(C(=O....
101 1FD0 Kd ~ 4 nM 254 C26 H27 N O3 CC1(CCC(c2....
102 1FCX Kd = 64 nM 184 C26 H28 O3 CC1(CCC(c2....
103 1EXA - 394 C23 H26 F N O4 CC1(CCC(c2....
104 1EXX - 961 C23 H26 F N O4 CC1(CCC(c2....
105 5M24 - 9CR C20 H28 O2 CC1=C(C(CC....
106 1FCY Kd = 3 nM 564 C26 H26 O3 CC1(CCC(c2....
107 1N46 Ki = 0.03 nM PFA C20 H21 N3 O4 Cc1cc(cc(c....
108 2PIN - LEG C15 H20 O CCCCCCc1cc....
109 3GWS - T3 C15 H12 I3 N O4 c1cc(c(cc1....
110 2J4A - OEF C18 H18 Br2 O4 CC(C)c1cc(....
111 3D57 - 4HY C14 H9 I3 O4 c1cc(c(cc1....
112 1XZX Kd = 0.06 nM T3 C15 H12 I3 N O4 c1cc(c(cc1....
113 3JZC ic50 ~ 1 nM 4HY C14 H9 I3 O4 c1cc(c(cc1....
114 1NQ0 - 4HY C14 H9 I3 O4 c1cc(c(cc1....
115 3CS4 - COV C28 H44 O4 C[C@]12CCC....
116 1S19 - MC9 C27 H40 O3 C[C@H](C=C....
117 3M7R - VDX C27 H44 O3 C[C@H](CCC....
118 3A40 - 23R C29 H46 O4 C[C@H]1[C@....
119 3TKC - FMV C28 H40 O4 C[C@H](c1c....
120 4ITE - TEY C30 H48 N4 O3 C[C@H](CCC....
121 3P8X - ZYD C27 H44 O3 CC(C)(CCCC....
122 1M13 Kd = 27 nM HYF C35 H52 O4 CC(C)C(=O)....
123 4X1F Ki = 11.5 uM 3WF C20 H24 O2 C[C@]12CC[....
124 5K13 Ki = 1.8 nM 6Q7 C27 H26 N2 O4 S CC(C)(C)c1....
125 1UPV - 444 C17 H12 F9 N O3 S c1ccc(cc1)....
126 3KFC ic50 = 2.8 nM 61X C23 H16 F3 N O3 S CS(=O)(=O)....
127 1XAP Kd = 2.5 nM TTB C24 H28 O2 C/C(=Cc1cc....
128 2LBD - REA C20 H28 O2 CC1=C(C(CC....
129 4LBD - 961 C23 H26 F N O4 CC1(CCC(c2....
130 5GID Kd = 769.2 nM VDP C37 H53 N O4 C[C@H](C[C....
131 5GIC Kd = 330.9 nM DLC C35 H51 N O4 C[C@H]1/C(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: VDP; Similar ligands found: 15
No: Ligand ECFP6 Tc MDL keys Tc
1 VDP 1 1
2 DLC 0.541353 0.967742
3 TEJ 0.528455 0.65625
4 VDX 0.520661 0.634921
5 TX5 0.495935 0.609375
6 ZNE 0.485075 0.701493
7 MC9 0.471545 0.603175
8 KH1 0.469231 0.630769
9 JC1 0.464567 0.630769
10 BIV 0.464 0.634921
11 7ZU 0.459677 0.603175
12 FMV 0.457364 0.671875
13 EB1 0.439394 0.619048
14 91W 0.434109 0.640625
15 ICJ 0.432836 0.625
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5GIC; Ligand: DLC; Similar sites found: 74
This union binding pocket(no: 1) in the query (biounit: 5gic.bio1) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3KYQ DPV 0.02304 0.41559 None
2 3CYI ATP 0.0315 0.41128 None
3 1X8D RNS 0.04276 0.40373 None
4 4RJD TFP 0.03718 0.40124 None
5 5UC9 MYR 0.04882 0.40008 1.76991
6 4MRP GSH 0.006111 0.44404 1.79153
7 5VRH OLB 0.03452 0.4087 2.8
8 3G58 988 0.02496 0.40574 3.2
9 4JZB P2H 0.02714 0.40029 3.2
10 1DZT TPE 0.02353 0.41329 3.27869
11 2F7A BEZ 0.01343 0.43416 3.44828
12 2GBB CIT 0.03042 0.40511 3.84615
13 2BP1 FLC 0.01048 0.42893 4
14 1DMY AZM 0.02567 0.40511 4.03226
15 4UBS DIF 0.03707 0.40013 4.4
16 5DCH 1YO 0.03831 0.40362 4.6875
17 5HCN DAO 0.04249 0.40133 5.6
18 2B4B B33 0.03975 0.40557 5.84795
19 4OUE IPT 0.02972 0.41206 6
20 1XZ3 ICF 0.01733 0.44211 6.32184
21 4X8D AVI 0.007497 0.42751 6.8
22 2QJY UQ2 0.04163 0.40332 6.95187
23 5MWE TCE 0.02048 0.41832 7.14286
24 3G5N PB2 0.03444 0.40714 7.2
25 1ECM TSA 0.01485 0.42132 7.33945
26 3HP9 CF1 0.04835 0.40565 7.6
27 4RW3 TDA 0.03675 0.40069 8.4
28 1RL4 BRR 0.03436 0.40629 9.04255
29 3KP6 SAL 0.01187 0.43936 9.93377
30 5M0T AKG 0.01776 0.42485 10.4
31 1U3R 338 0.0005746 0.46781 12.8631
32 2VWA PTY 0.01879 0.42123 12.8713
33 5OCA 9QZ 0.00306 0.46223 12.9032
34 3UP3 XCA 0.003762 0.41338 13.1687
35 3QM1 ZYC 0.02059 0.40625 14
36 3RV5 DXC 0.0371 0.40728 15.7303
37 2BJ4 OHT 0.001127 0.44618 16.8
38 1NCQ W11 0.01443 0.40026 23.5294
39 1PZL MYR 0.002535 0.4382 29.1139
40 3GYT DL4 0.0004608 0.45134 30.3279
41 4QJR PIZ 0.004656 0.40382 31.4286
42 1ZDT PEF 0.002028 0.41537 31.9502
43 5HCV 60R 0.002073 0.4345 32
44 2A3I C0R 0.002123 0.43046 32
45 1G2N EPH 0.001022 0.43696 32.5758
46 1FBY REA 0.002119 0.42376 33.0544
47 4WPF 3SN 0.0006039 0.45018 33.6
48 5X8Q 82R 0.0001283 0.42797 33.6
49 1YMT DR9 0.001991 0.40701 34.5528
50 1YP0 PEF 0.006286 0.40701 35.5649
51 1N83 CLR 0.001417 0.42775 36.8
52 3ET1 ET1 0.0004547 0.401 37.2
53 1N4H REA 0.0002526 0.46623 37.6
54 1YOK P6L 0.001712 0.42053 38.4
55 1YUC EPH 0.002875 0.40939 38.4
56 1NQ7 ARL 0.002272 0.43275 38.5246
57 5UNJ RJW 0.003207 0.43746 39.1837
58 1HG4 LPP 0.0004506 0.44113 39.6
59 3ET3 ET1 0.004772 0.41852 40.8
60 3G9E RO7 0.0007416 0.43214 41.2
61 1FM9 9CR 0.004416 0.42001 41.2
62 2PRG BRL 0.01515 0.40242 41.2
63 2QA8 GEN 0.00008502 0.51727 42.8
64 3UUA 0CZ 0.0001362 0.50745 42.8
65 3UUD EST 0.0003534 0.4876 42.8
66 3UU7 2OH 0.002014 0.47173 42.8
67 2QZO KN1 0.001781 0.44124 42.8
68 4DM8 REA 0.00008793 0.48565 43.2
69 3BEJ MUF 0.0003141 0.46221 44.5378
70 4DK7 0KS 0.000006877 0.54977 44.9393
71 3OKI OKI 0.00574 0.41498 45.0644
72 3DCT 064 0.0001252 0.47079 45.1064
73 5ICK FEZ 0.0003757 0.47164 46.2882
74 3RUU 37G 0.0001133 0.46105 46.2882
75 3KMR EQN 0.00002428 0.52513 50
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