Receptor
PDB id Resolution Class Description Source Keywords
5D3X 1.69 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE P-REX1 PH DOMAIN WITH INOSITOL-(1,3 TETRAKISPHOSPHATE BOUND HOMO SAPIENS PLECKSTRIN HOMOLOGY DOMAIN BETA SANDWICH PHOSPHATIDYLINOSIBINDING LIPID BINDING PROTEIN
Ref.: STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF THE CORE OF THE METASTATIC FACTOR P-REX1 AND ITS REGULA PTDINS(3,4,5)P3. STRUCTURE V. 24 730 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
4IP A:501;
B:501;
Valid;
Valid;
none;
none;
Kd = 440 nM
500.075 C6 H16 O18 P4 [C@H]...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5D3X 1.69 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE P-REX1 PH DOMAIN WITH INOSITOL-(1,3 TETRAKISPHOSPHATE BOUND HOMO SAPIENS PLECKSTRIN HOMOLOGY DOMAIN BETA SANDWICH PHOSPHATIDYLINOSIBINDING LIPID BINDING PROTEIN
Ref.: STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF THE CORE OF THE METASTATIC FACTOR P-REX1 AND ITS REGULA PTDINS(3,4,5)P3. STRUCTURE V. 24 730 2016
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 5D3X Kd = 440 nM 4IP C6 H16 O18 P4 [C@H]1([C@....
2 5D3Y Kd = 440 nM 4IP C6 H16 O18 P4 [C@H]1([C@....
3 5D3V - FLC C6 H5 O7 C(C(=O)[O-....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 5D3X Kd = 440 nM 4IP C6 H16 O18 P4 [C@H]1([C@....
2 5D3Y Kd = 440 nM 4IP C6 H16 O18 P4 [C@H]1([C@....
3 5D3V - FLC C6 H5 O7 C(C(=O)[O-....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 5D3X Kd = 440 nM 4IP C6 H16 O18 P4 [C@H]1([C@....
2 5D3Y Kd = 440 nM 4IP C6 H16 O18 P4 [C@H]1([C@....
3 5D3V - FLC C6 H5 O7 C(C(=O)[O-....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 4IP; Similar ligands found: 15
No: Ligand ECFP6 Tc MDL keys Tc
1 4IP 1 1
2 I3P 0.724138 0.966667
3 I3S 0.724138 0.966667
4 5MY 0.714286 0.965517
5 5IP 0.714286 0.965517
6 IP5 0.714286 0.965517
7 I5P 0.714286 0.965517
8 I4P 0.653846 0.965517
9 I0P 0.62069 0.933333
10 ITP 0.6 0.966667
11 2IP 0.571429 0.966667
12 IHP 0.538462 0.965517
13 I6P 0.538462 0.965517
14 IP2 0.533333 0.966667
15 I4D 0.516129 0.933333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5D3X; Ligand: 4IP; Similar sites found: 59
This union binding pocket(no: 1) in the query (biounit: 5d3x.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2GJ5 VD3 0.006468 0.46197 None
2 2FXD DR7 0.01859 0.41733 None
3 1MAI I3P 0.004865 0.41141 None
4 1SIV PSI 0.02822 0.4071 None
5 3S43 478 0.02472 0.40567 None
6 3FSM 2NC 0.03531 0.40525 None
7 5C1P DAL DAL 0.04646 0.40144 None
8 5UR1 YY9 0.04616 0.40689 1.79641
9 4ZU4 4TG 0.007691 0.42186 2.02703
10 1NYW DAU 0.008382 0.42962 2.39521
11 1DMY AZM 0.01272 0.40782 2.39521
12 1ZM1 BGC BGC BGC 0.001179 0.47305 2.99401
13 5MJA 7O3 0.00576 0.43149 2.99401
14 1RQJ RIS 0.01795 0.41484 2.99401
15 1IDA 0PO 0.03764 0.40046 3.0303
16 1IOW PHY 0.008492 0.44379 3.59281
17 1IOW ADP 0.008492 0.44379 3.59281
18 2HK5 1BM 0.009475 0.43372 3.59281
19 1RE8 BD2 0.04698 0.4009 3.59281
20 1GZF NAD 0.02436 0.408 3.79147
21 1UPR 4IP 0.000003564 0.5594 4.06504
22 3FW9 SLX 0.009631 0.41838 4.19162
23 3IU9 T07 0.0415 0.40469 4.19162
24 4NFN 2KC 0.003199 0.45345 4.79042
25 4QJP V1F 0.005318 0.4484 4.79042
26 4MAE PQQ 0.008531 0.42162 4.79042
27 2RKV COA 0.02579 0.41324 4.79042
28 4GGZ BTN 0.008882 0.40744 5.21739
29 4IGH 1EA 0.04723 0.42044 5.38922
30 4IGH FMN 0.04723 0.42044 5.38922
31 4IGH ORO 0.04723 0.42044 5.38922
32 3MWS 017 0.02912 0.40544 5.38922
33 1OJK GLC BGC 0.009051 0.40328 5.38922
34 1KOJ PAN 0.002042 0.44461 5.98802
35 5UI2 EQ3 0.0216 0.41407 5.98802
36 1RSG FAD 0.03194 0.41176 5.98802
37 2A9K NAD 0.02709 0.40499 5.98802
38 3ML5 AZM 0.008474 0.41074 6.58683
39 2VCH UDP 0.04776 0.40252 6.58683
40 3EEB IHP 0.008581 0.41582 6.69856
41 1FAO 4IP 0.0001942 0.48449 7.14286
42 5H2U 1N1 0.01073 0.42183 7.18563
43 1JS4 BGC BGC 0.03853 0.40544 7.18563
44 1JS4 BGC 0.04067 0.40544 7.18563
45 4FIL 0UE 0.0175 0.40111 7.18563
46 4RFR RHN 0.01037 0.4305 8.38323
47 4WZH FMN 0.0338 0.40764 8.38323
48 1QPR PPC 0.005235 0.43451 8.98204
49 1JCM 137 0.003161 0.42406 8.98204
50 1W1G 4PT 0.000002049 0.58437 9.27152
51 4EMV 0R9 0.01911 0.40576 9.58084
52 4AX7 4MU BGC BGC 0.03092 0.40035 9.58084
53 1W6S PQQ 0.01309 0.40548 12.1622
54 1FHX 4IP 0.0004285 0.40323 12.4031
55 4KYS VIB 0.0177 0.40381 12.5749
56 4OYA 1VE 0.01121 0.4482 15.5689
57 1F76 FMN 0.02855 0.40434 17.3653
58 1U29 I3P 0.0007224 0.45758 27.5449
59 1FHW I5P 0.0001657 0.49412 32.3353
Pocket No.: 2; Query (leader) PDB : 5D3X; Ligand: 4IP; Similar sites found: 25
This union binding pocket(no: 2) in the query (biounit: 5d3x.bio2) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3I59 N6R 0.004183 0.4537 None
2 3FW4 CAQ 0.01868 0.41334 None
3 4LSY FLC 0.002471 0.40048 None
4 3NNT DQA 0.009386 0.40716 1.79641
5 1FRB ZST 0.04838 0.40208 1.79641
6 3ETH ATP 0.01378 0.40661 2.39521
7 3B1Q NOS 0.01579 0.41258 2.99401
8 3F5O UOC COA 0.04761 0.40416 3.37838
9 2OFV 242 0.01811 0.4178 3.59281
10 2FTB OLA 0.04274 0.4075 4
11 3JU6 ANP 0.004592 0.42244 4.19162
12 3WUC GLC GAL 0.009991 0.42395 4.37956
13 4WOE ADP 0.002343 0.43114 4.79042
14 3AJH BL3 0.01431 0.41676 4.79042
15 1M15 ADP 0.02183 0.40734 4.79042
16 1M15 ARG 0.02183 0.40734 4.79042
17 5M06 ADP 0.0111 0.40681 5.38922
18 3GD9 GLC BGC BGC BGC 0.01982 0.41066 6.58683
19 1OLM VTQ 0.01856 0.4126 7.18563
20 3WUD GLC GAL 0.01879 0.40324 7.18563
21 3SXS PP2 0.01275 0.42395 7.78443
22 4P8K FAD 0.04947 0.41571 8.38323
23 4P8K 38C 0.04947 0.41571 8.38323
24 5N0F 7K2 0.02176 0.40799 10.1796
25 2D0V PQQ 0.02044 0.40856 15.5689
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