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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 1443 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 1205 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 1039 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 I3S 0.724138 0.966667
3 I3P 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 with APoc: 124
This union binding pocket(no: 1) in the query (biounit: 5d3x.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 2GJ5 VD3 None
2 4IEN GDP None
3 5XEG AKG None
4 2FXD DR7 None
5 1F5V FMN None
6 1MAI I3P None
7 1SIV PSI None
8 3S43 478 None
9 3FSM 2NC None
10 5C1P DAL DAL None
11 2AZC 3TL None
12 1TKK ALA GLU 1.1976
13 5UR1 YY9 1.79641
14 4ZU4 4TG 2.02703
15 1VPM COA 2.39521
16 1NYW DAU 2.39521
17 1EHI PHY 2.39521
18 6GWR FEW 2.39521
19 1DMY AZM 2.39521
20 1ZM1 BGC BGC BGC 2.99401
21 6GQM F8H 2.99401
22 6DAM PQQ 2.99401
23 5MJA 7O3 2.99401
24 4WW8 VD9 2.99401
25 1RQJ RIS 2.99401
26 1IDA 0PO 3.0303
27 3WSJ MK1 3.44828
28 1IOW ADP 3.59281
29 1IOW PHY 3.59281
30 4KBA 1QM 3.59281
31 5W4W 9WG 3.59281
32 1UNB PN1 3.59281
33 1UNB AKG 3.59281
34 5XM3 PQQ 3.59281
35 3FW3 ETS 3.59281
36 3N2S FMN 3.59281
37 1RE8 BD2 3.59281
38 1GZF NAD 3.79147
39 1UPR 4IP 4.06504
40 5FBN 5WF 4.19162
41 3FW9 SLX 4.19162
42 2VQ5 HBA 4.19162
43 4P6C RES 4.19162
44 6FE1 V14 4.19162
45 3IU9 T07 4.19162
46 6FOF LAT 4.19162
47 1LTH NAD 4.19162
48 4EWH T77 4.79042
49 4NFN 2KC 4.79042
50 5E2N V14 4.79042
51 4I9A NCN 4.79042
52 6FKW PQQ 4.79042
53 2RKV COA 4.79042
54 1TV5 FMN 4.79042
55 5NQR 958 4.79042
56 1K97 CIR 4.79042
57 1K97 ASP 4.79042
58 1TID ATP 5.14706
59 4GGZ BTN 5.21739
60 1OPK P16 5.38922
61 3WDM ADN 5.38922
62 3MWS 017 5.38922
63 1OJK GLC BGC 5.38922
64 1CQ1 BGC 5.38922
65 1KOJ PAN 5.98802
66 1EP2 FMN 5.98802
67 4NW6 2NS 5.98802
68 3PFG TLO 5.98802
69 3PFG SAM 5.98802
70 5TUX ECH 5.98802
71 1O98 2PG 5.98802
72 5UI2 EQ3 5.98802
73 1EP2 ORO 5.98802
74 2CXS F6P 5.98802
75 1RSG FAD 5.98802
76 5TZO 7V7 5.98802
77 2A9K NAD 5.98802
78 3VSV XYP 6.58683
79 2VFT SOR 6.58683
80 1GTE FMN 6.58683
81 1GTE IUR 6.58683
82 1G72 PQQ 6.58683
83 1JSH SIA GAL 6.58683
84 2VCH UDP 6.58683
85 3EEB IHP 6.69856
86 1FAO 4IP 7.14286
87 5H2U 1N1 7.18563
88 1E4E PHY 7.18563
89 1JS4 BGC 7.18563
90 1JS4 BGC BGC 7.18563
91 4FIL 0UE 7.18563
92 1LRW PQQ 7.22892
93 1JQY A32 7.76699
94 6CLV 6MB 7.78443
95 1ULE GLA GAL NAG 7.78443
96 1UNQ 4IP 8
97 3GC8 B45 8.38323
98 4RFR RHN 8.38323
99 3R35 4CO 8.38323
100 4WZH FMN 8.38323
101 6GIN IR2 8.98204
102 1QPR PPC 8.98204
103 1JCM 137 8.98204
104 4YGF AZM 8.98204
105 1W1G 4PT 9.27152
106 4EMV 0R9 9.58084
107 6HDT BTN 9.58084
108 4AX7 4MU BGC BGC 9.58084
109 2P8B NSK 10.7784
110 5NCJ SIN 11.976
111 4OAV PO4 PO4 A A A A PO4 11.976
112 1W6S PQQ 12.1622
113 1FHX 4IP 12.4031
114 1B55 4IP 12.5749
115 3IGZ 3PG 12.5749
116 3IGZ 2PG 12.5749
117 6E08 NAP 12.5749
118 4KYS VIB 12.5749
119 3DER ALA LYS 14.3713
120 4OYA 1VE 15.5689
121 2D0V PQQ 15.5689
122 1F76 FMN 17.3653
123 1U29 I3P 27.5449
124 1FHW I5P 32.3353
Pocket No.: 2; Query (leader) PDB : 5D3X; Ligand: 4IP; Similar sites found with APoc: 43
This union binding pocket(no: 2) in the query (biounit: 5d3x.bio2) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 3I59 N6R None
2 3EM0 CHD None
3 3FW4 CAQ None
4 2ED4 FAD None
5 4LSY FLC None
6 3NNT DQA 1.79641
7 1FRB ZST 1.79641
8 3ETH ATP 2.39521
9 3B1Q NOS 2.99401
10 3F5O UOC COA 3.37838
11 5M77 7K2 7K3 3.59281
12 2OFV 242 3.59281
13 2FTB OLA 4
14 3JU6 ANP 4.19162
15 2X41 BGC 4.19162
16 3WUC GLC GAL 4.37956
17 2WLG SOP 4.79042
18 4C5N ACP 4.79042
19 3AJH BL3 4.79042
20 1M15 ARG 4.79042
21 1M15 ADP 4.79042
22 4WOE ADP 4.79042
23 5M06 ADP 5.38922
24 4HWT 1B2 5.38922
25 2PO3 T4K 5.98802
26 3JQ3 ADP 6.58683
27 3GD9 GLC BGC BGC BGC 6.58683
28 1OLM VTQ 7.18563
29 4R4U COA 7.18563
30 5JZI LYS LEU VAL ALA LEU GLY ILE ASN ALA VAL 7.18563
31 4TR9 38D 7.18563
32 3SXS PP2 7.78443
33 5AK8 ALA ARG 7.78443
34 4P8K FAD 8.38323
35 4P8K 38C 8.38323
36 4BG4 ADP 8.38323
37 5N0L ILE 8.80503
38 1E8G FCR 8.98204
39 5O9X G16 9.58084
40 6F5W KG1 9.58084
41 5N0F 7K2 10.1796
42 5B48 TDN 16.1677
43 5N9T 8QQ 20.9581
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