Receptor
PDB id Resolution Class Description Source Keywords
6F30 2.3 Å EC: 3.1.4.1 CRYSTAL STRUCTURE OF ECTONUCLEOTIDE PHOSPHODIESTERASE/PYROPH 3 (NPP3) IN COMPLEX WITH UDPGLCNAC RATTUS NORVEGICUS ENZYME ECTONUCLEOTIDE PHOSPHODIESTERASE/PYROPHOSPHATASE CYPROTEIN HYDROLASE
Ref.: CRYSTAL STRUCTURE AND SUBSTRATE BINDING MODE OF ECTONUCLEOTIDE PHOSPHODIESTERASE/PYROPHOSPHATASE-3 SCI REP V. 8 10874 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAG B:1013;
B:1008;
B:1007;
B:1012;
A:1013;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
 submit data
221.208 C8 H15 N O6 CC(=O...
NAG NAG G:1;
D:1;
C:1;
F:1;
E:1;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
 submit data
408.404 n/a O=C(N...
CA A:1004;
B:1004;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
40.078 Ca [Ca+2...
UD1 B:1001;
A:1001;
 Valid;
Valid;
 none;
none;
 submit data
607.354 C17 H27 N3 O17 P2 CC(=O...
NAG NAG BMA H:1;
 Invalid;
 none;
 submit data
570.545 n/a O=C(N...
ZN B:1003;
A:1002;
B:1002;
A:1003;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
 submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6F30 2.3 Å EC: 3.1.4.1 CRYSTAL STRUCTURE OF ECTONUCLEOTIDE PHOSPHODIESTERASE/PYROPH 3 (NPP3) IN COMPLEX WITH UDPGLCNAC RATTUS NORVEGICUS ENZYME ECTONUCLEOTIDE PHOSPHODIESTERASE/PYROPHOSPHATASE CYPROTEIN HYDROLASE
Ref.: CRYSTAL STRUCTURE AND SUBSTRATE BINDING MODE OF ECTONUCLEOTIDE PHOSPHODIESTERASE/PYROPHOSPHATASE-3 SCI REP V. 8 10874 2018
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 6F2V - AMP C10 H14 N5 O7 P c1nc(c2c(n....
2 6F2Y - B4P C20 H28 N10 O19 P4 c1nc(c2c(n....
3 6F30 - UD1 C17 H27 N3 O17 P2 CC(=O)N[C@....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6F2V - AMP C10 H14 N5 O7 P c1nc(c2c(n....
2 6F2Y - B4P C20 H28 N10 O19 P4 c1nc(c2c(n....
3 6F30 - UD1 C17 H27 N3 O17 P2 CC(=O)N[C@....
4 6C02 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
50% Homology Family (29)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5M0D - 7C8 C36 H54 Cl2 N2 O4 C[C@H](CCC....
2 4ZG6 ic50 = 0.011 uM 4NY C25 H16 Cl F N2 O2 c1cc(ccc1C....
3 6W35 Ki = 12 nM SKV C28 H28 F4 N6 O4 CC(C)[C@H]....
4 5DLT - 5JK C27 H46 O2 C[C@H](CCC....
5 5OLB - 6ZO C22 H21 Cl2 N3 O5 c1cc2c(cc1....
6 5IJQ - 5JK C27 H46 O2 C[C@H](CCC....
7 3WAX ic50 = 13 nM DWX C21 H20 B Cl2 N3 O3 S B(c1cccc(c....
8 6LEH ic50 = 3.3 nM EAR C17 H16 Cl N3 O3 CCOC(=O)CN....
9 5L0B ic50 = 520 nM 6ZM C18 H20 N4 O CC(=O)N1CC....
10 5M0M - 7CF C36 H52 Cl2 N2 O5 C[C@H](CCC....
11 5LIA ic50 = 0.001 uM 6XN C25 H22 Cl F3 N4 O2 C[C@@H](c1....
12 5DLW Ki = 9 uM 5D5 C26 H45 N O6 S C[C@H](CCC....
13 5LQQ ic50 = 81 nM 72P C22 H16 Cl N O2 S Cc1c(c2ccc....
14 5IJS - 5JK C27 H46 O2 C[C@H](CCC....
15 4ZG7 ic50 = 0.002 uM 4O0 C28 H21 Cl F2 N2 O3 S Cc1c(c2ccc....
16 3WAW ic50 = 580 nM DWW C21 H20 B Cl2 N3 O3 S B(c1ccccc1....
17 3WAV ic50 = 180 nM DWV C15 H15 Cl2 N3 O S CN1CCN(CC1....
18 6Y5M ic50 = 9.6 nM O9W C24 H26 Cl F N6 O Cc1nnn(n1)....
19 5M0S - 7CW C34 H50 Cl2 N2 O5 C[C@H](CCC....
20 5MHP Ki = 15 nM 7NB C30 H33 F N8 O2 S CCc1c(n2cc....
21 5OHI - 9V8 C23 H19 F6 N5 O3 c1cc2c(cc1....
22 5M0E - 7CR C22 H23 Cl2 N3 O5 c1cc2c(cc1....
23 5DLV ic50 = 10.4 uM 5D5 C26 H45 N O6 S C[C@H](CCC....
24 6F2V - AMP C10 H14 N5 O7 P c1nc(c2c(n....
25 6F2Y - B4P C20 H28 N10 O19 P4 c1nc(c2c(n....
26 6F30 - UD1 C17 H27 N3 O17 P2 CC(=O)N[C@....
27 6AEK - A G n/a n/a
28 6AEL - 4BW C20 H24 N10 O13 P2 c1nc(c2c(n....
29 6C02 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: UD1; Similar ligands found: 83
No: Ligand ECFP6 Tc MDL keys Tc
1 UD2 1 1
2 UD1 1 1
3 UDZ 0.8 0.893333
4 HP7 0.793814 0.985294
5 EPZ 0.75 0.985507
6 EEB 0.742857 0.971429
7 EPU 0.742857 0.971429
8 F5P 0.742574 0.957143
9 F5G 0.742574 0.971014
10 UD4 0.742574 0.957143
11 UPG 0.73913 0.985294
12 GDU 0.73913 0.985294
13 UFM 0.73913 0.985294
14 UD7 0.722772 0.971014
15 MJZ 0.715686 0.957143
16 UPF 0.697917 0.930556
17 U2F 0.697917 0.930556
18 UMA 0.690265 0.985507
19 UDM 0.683168 0.957143
20 UFG 0.663265 0.930556
21 HWU 0.660377 0.943662
22 12V 0.660377 0.943662
23 AWU 0.659794 0.985294
24 U20 0.655462 0.871795
25 U21 0.655462 0.871795
26 U22 0.655462 0.85
27 UGA 0.65 0.970588
28 UGB 0.65 0.970588
29 USQ 0.633663 0.835443
30 UAD 0.63 0.956522
31 UDX 0.63 0.956522
32 UGF 0.627451 0.916667
33 UDP 0.622222 0.927536
34 UTP 0.619565 0.927536
35 UAG 0.617188 0.931507
36 U5F 0.612903 0.927536
37 URM 0.6 0.942857
38 660 0.6 0.942857
39 G3N 0.596154 0.929577
40 UPU 0.587629 0.955882
41 4RA 0.584615 0.87013
42 UNP 0.583333 0.901408
43 3UC 0.575472 0.930556
44 UML 0.564286 0.871795
45 IUG 0.561404 0.825
46 U5P 0.555556 0.913043
47 U 0.555556 0.913043
48 UDP GAL 0.552381 0.956522
49 UD0 0.552239 0.858974
50 UPP 0.543689 0.928571
51 UDH 0.543689 0.855263
52 2KH 0.530612 0.901408
53 44P 0.521277 0.888889
54 C5G 0.518519 0.930556
55 UDP UDP 0.505155 0.898551
56 Y6W 0.504673 0.90411
57 2QR 0.485075 0.860759
58 2GW 0.482759 0.943662
59 URI 0.477273 0.852941
60 UP5 0.47541 0.844156
61 PMP UD1 0.467626 0.848101
62 1GW 0.467213 0.905405
63 CJB 0.461538 0.838235
64 UAG API 0.457516 0.87013
65 4TC 0.456 0.822785
66 CSQ 0.452991 0.866667
67 CSV 0.452991 0.866667
68 U3P 0.447917 0.898551
69 UA3 0.447917 0.898551
70 GN1 0.444444 0.753623
71 NG1 0.444444 0.753623
72 C30 0.433628 0.696203
73 Q5S 0.433628 0.696203
74 FZK 0.431193 0.771084
75 PUP 0.429825 0.875
76 LSU 0.428571 0.732558
77 CXY 0.422414 0.90411
78 U2P 0.418367 0.913043
79 UMA FGA LYS DAL DAL 0.414634 0.8375
80 U1S 0.409091 0.789474
81 FN5 0.40458 0.883117
82 YSU 0.403361 0.741176
83 DAU 0.403361 0.905405
Similar Ligands (3D)
Ligand no: 1; Ligand: UD1; Similar ligands found: 2
No: Ligand Similarity coefficient
1 GDD 0.8671
2 TDX 0.8645
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6F30; Ligand: UD1; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 6f30.bio2) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 5EGH PC 44.7552
Pocket No.: 2; Query (leader) PDB : 6F30; Ligand: UD1; Similar sites found with APoc: 2
This union binding pocket(no: 2) in the query (biounit: 6f30.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
1 5EGH PC 44.7552
2 5EGH PC 44.7552
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