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Receptor
PDB id Resolution Class Description Source Keywords
3ZWO 2 Å EC: 3.2.2.5 CRYSTAL STRUCTURE OF ADP RIBOSYL CYCLASE COMPLEXED WITH REACTION INTERMEDIATE APLYSIA CALIFORNICA HYDROLASE CD38 HYDROLYSIS NAD SUBSTRATE SPECIFICITY
Ref.: STRUCTURAL STUDIES OF INTERMEDIATES ALONG THE CYCLI PATHWAY OF APLYSIA ADP-RIBOSYL CYCLASE. J.MOL.BIOL. V. 415 514 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
G2Q A:301;
B:301;
C:301;
E:301;
G:301;
H:301;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
submit data
559.316 C15 H23 N5 O14 P2 c1nc2...
NGD F:5573;
Valid;
none;
submit data
680.432 C21 H28 N7 O15 P2 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3I9L 1.75 Å EC: 3.2.2.5 CRYSTAL STRUCTURE OF ADP RIBOSYL CYCLASE COMPLEXED WITH N1-C APLYSIA CALIFORNICA HOMODIMER ENZYME-PRODUCT ANALOG COMPLEX ADP-RIBOSYL CYCLASDISULFIDE BOND FERTILIZATION HYDROLASE NAD
Ref.: STRUCTURAL BASIS FOR ENZYMATIC EVOLUTION FROM A DED ADP-RIBOSYL CYCLASE TO A MULTIFUNCTIONAL NAD HYDROL J.BIOL.CHEM. V. 284 27637 2009
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3I9L - N1C C15 H20 N4 O14 P2 c1nc2c3n1[....
2 1R15 - NCA C6 H6 N2 O c1cc(cnc1)....
3 3ZWO - NGD C21 H28 N7 O15 P2 c1cc(c[n+]....
4 3ZWN - NGD C21 H28 N7 O15 P2 c1cc(c[n+]....
5 3I9K - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
6 1R16 - PYF C6 H7 N O c1cc(cnc1)....
7 3ZWM - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
8 3I9J - NCA C6 H6 N2 O c1cc(cnc1)....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3I9L - N1C C15 H20 N4 O14 P2 c1nc2c3n1[....
2 1R15 - NCA C6 H6 N2 O c1cc(cnc1)....
3 3ZWO - NGD C21 H28 N7 O15 P2 c1cc(c[n+]....
4 3ZWN - NGD C21 H28 N7 O15 P2 c1cc(c[n+]....
5 3I9K - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
6 1R16 - PYF C6 H7 N O c1cc(cnc1)....
7 3ZWM - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
8 3I9J - NCA C6 H6 N2 O c1cc(cnc1)....
50% Homology Family (27)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1ISI - NCA C6 H6 N2 O c1cc(cnc1)....
2 1ISJ - NMN C11 H16 N2 O8 P c1cc(c[n+]....
3 1ISH - ENP C17 H24 N5 O17 P3 c1cn2cnc3c....
4 3I9L - N1C C15 H20 N4 O14 P2 c1nc2c3n1[....
5 1R15 - NCA C6 H6 N2 O c1cc(cnc1)....
6 3ZWO - NGD C21 H28 N7 O15 P2 c1cc(c[n+]....
7 3ZWN - NGD C21 H28 N7 O15 P2 c1cc(c[n+]....
8 3I9K - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
9 1R16 - PYF C6 H7 N O c1cc(cnc1)....
10 3ZWM - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
11 3I9J - NCA C6 H6 N2 O c1cc(cnc1)....
12 4OGW - NMN C11 H16 N2 O8 P c1cc(c[n+]....
13 3ROP - NCA C6 H6 N2 O c1cc(cnc1)....
14 3DZG - NCA C6 H6 N2 O c1cc(cnc1)....
15 2HCT - NMN C11 H16 N2 O8 P c1cc(c[n+]....
16 2I66 - G1R G1R n/a n/a
17 2O3S - CXR C15 H21 N5 O13 P2 [H]/N=C/1c....
18 3DZI - RGT C15 H25 N5 O21 P4 c1nc2c(n1[....
19 2I67 - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
20 3DZK - NMN C11 H16 N2 O8 P c1cc(c[n+]....
21 3DZH - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
22 4TMF - JS2 C14 H23 N5 O12 P2 C1=Nc2c(nc....
23 2PGJ ic50 = 0.26 mM N1C C15 H20 N4 O14 P2 c1nc2c3n1[....
24 3DZJ - NMN C11 H16 N2 O8 P c1cc(c[n+]....
25 2O3Q - CXR C15 H21 N5 O13 P2 [H]/N=C/1c....
26 2O3T - CGR C15 H23 N5 O14 P2 C1[C@@H]2[....
27 2I65 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: G2Q; Similar ligands found: 55
No: Ligand ECFP6 Tc MDL keys Tc
1 G2Q 1 1
2 G2R 0.646465 1
3 C1Z 0.576923 0.948052
4 6CG 0.574468 0.8875
5 AVV 0.543689 0.865854
6 G1R 0.495238 0.948718
7 GP3 0.490196 0.936709
8 GTP 0.471698 0.961039
9 GDP 0.471154 0.961039
10 GNH 0.466667 0.948718
11 GSP 0.462963 0.91358
12 9GM 0.462963 0.936709
13 GNP 0.462963 0.936709
14 6CE 0.455285 0.818182
15 GCP 0.453704 0.961538
16 AJQ 0.451613 0.858824
17 Y9Z 0.448276 0.892857
18 GNG 0.447917 0.860759
19 NA7 0.433628 0.923077
20 GMV 0.431193 0.936709
21 A2D 0.43 0.860759
22 GPD 0.429752 0.914634
23 GDX 0.429752 0.936709
24 6CK 0.428571 0.902439
25 GKE 0.423729 0.925
26 GDC 0.423729 0.925
27 GDD 0.423729 0.925
28 5GP 0.423077 0.948052
29 G 0.423077 0.948052
30 R7I 0.422018 0.910256
31 R5I 0.422018 0.910256
32 NGD 0.420635 0.925
33 GTG 0.420168 0.902439
34 GFB 0.420168 0.925
35 GDR 0.420168 0.925
36 G3A 0.416667 0.936709
37 APR 0.415094 0.860759
38 AR6 0.415094 0.860759
39 GPG 0.413793 0.925
40 93A 0.413462 0.804598
41 G5P 0.413223 0.936709
42 G2P 0.410714 0.974359
43 GKD 0.409836 0.925
44 JB2 0.409836 0.925
45 MGP 0.409091 0.925
46 BA3 0.407767 0.860759
47 6G0 0.405405 0.925
48 B4P 0.403846 0.860759
49 AP5 0.403846 0.860759
50 GP2 0.40367 0.974359
51 A1R 0.403509 0.876543
52 GAV 0.403509 0.925
53 JB3 0.401575 0.91358
54 AT4 0.4 0.851852
55 2MD 0.4 0.860465
Ligand no: 2; Ligand: NGD; Similar ligands found: 111
No: Ligand ECFP6 Tc MDL keys Tc
1 NGD 1 1
2 GP3 0.673267 0.987013
3 G1R 0.657143 0.948718
4 G2R 0.651376 0.925
5 GDP 0.650485 0.961039
6 GTP 0.647619 0.961039
7 GNH 0.644231 0.948718
8 GSP 0.635514 0.91358
9 GCP 0.626168 0.936709
10 Y9Z 0.622807 0.870588
11 9GM 0.62037 0.936709
12 GNP 0.62037 0.936709
13 GTG 0.617391 0.974684
14 G 0.601942 0.948052
15 5GP 0.601942 0.948052
16 GMV 0.601852 0.936709
17 GDX 0.583333 0.961538
18 GKE 0.581197 0.949367
19 GDC 0.581197 0.949367
20 GDD 0.581197 0.949367
21 GFB 0.576271 0.949367
22 GDR 0.576271 0.949367
23 GKD 0.575 0.949367
24 NAD 0.574803 0.922078
25 GP2 0.574074 0.925
26 JB3 0.572581 0.9375
27 G3A 0.571429 0.987013
28 6CK 0.571429 0.925926
29 GPD 0.570248 0.914634
30 G5P 0.566667 0.987013
31 GAV 0.566372 0.925
32 NFD 0.565891 0.876543
33 G2P 0.5625 0.925
34 NHD 0.5625 0.897436
35 JB2 0.561983 0.949367
36 DND 0.560976 0.923077
37 NXX 0.560976 0.923077
38 GPG 0.560345 0.974359
39 DBG 0.552239 0.962025
40 8ID 0.552 0.901235
41 NAJ 0.546875 0.922078
42 YGP 0.546219 0.891566
43 ALF 5GP 0.544643 0.879518
44 2MD 0.542636 0.882353
45 MGD 0.541985 0.882353
46 FEG 0.53125 0.892857
47 CAG 0.530303 0.916667
48 ALF GDP 0.529915 0.879518
49 GDP ALF 0.529915 0.879518
50 GDP AF3 0.529915 0.879518
51 GDP 7MG 0.528455 0.949367
52 ZGP 0.527132 0.882353
53 CG2 0.523077 0.925926
54 PGD 0.514706 0.914634
55 MD1 0.514706 0.882353
56 NMN 0.514563 0.831169
57 G3D 0.508621 0.948052
58 0O2 0.508333 0.948052
59 U2G 0.507692 0.925926
60 TPG 0.507246 0.833333
61 G G 0.5 0.987013
62 G4P 0.5 0.948052
63 A3D 0.496296 0.910256
64 GMP 0.495146 0.846154
65 NAP 0.485714 0.935065
66 FE9 0.485507 0.789474
67 GH3 0.478992 0.935897
68 NDO 0.478571 0.910256
69 3GP 0.468468 0.910256
70 G1G 0.467626 0.9625
71 CNA 0.466667 0.923077
72 BGO 0.462687 0.9375
73 A G 0.459854 0.974026
74 AMP NAD 0.459854 0.897436
75 NBP 0.458333 0.901235
76 U A G G 0.456522 0.974026
77 GCP G 0.456 0.910256
78 G4M 0.453333 0.894118
79 GGM 0.452555 0.914634
80 DGT 0.45 0.888889
81 GPX 0.447154 0.910256
82 MGP 0.445378 0.949367
83 6G0 0.441667 0.949367
84 DGI 0.440678 0.888889
85 G A A A 0.438849 0.961538
86 G1R G1R 0.434483 0.962025
87 R5I 0.433333 0.910256
88 R7I 0.433333 0.910256
89 PGD O 0.431507 0.863636
90 AKW 0.430657 0.926829
91 2GP 0.429825 0.923077
92 ZID 0.424658 0.935065
93 IDP 0.423729 0.935065
94 NNR 0.421569 0.705128
95 G C 0.421429 0.91358
96 GTA 0.421053 0.974684
97 G2Q 0.420635 0.925
98 NA0 0.418919 0.923077
99 G U 0.417266 0.91358
100 9JJ 0.417178 0.879518
101 NCN 0.414414 0.74359
102 GPC 0.412587 0.870588
103 TAP 0.412162 0.876543
104 G G G RPC 0.411348 0.9125
105 N01 0.409722 0.897436
106 NAQ 0.408163 0.888889
107 DGP 0.401709 0.876543
108 G7M 0.401709 0.936709
109 DG 0.401709 0.876543
110 A G C C 0.401361 0.925
111 NAE 0.401361 0.911392
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3I9L; Ligand: N1C; Similar sites found with APoc: 22
This union binding pocket(no: 1) in the query (biounit: 3i9l.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 4Z7X 3CX 1.68067
2 3VOZ 04A 2.32558
3 1MFI FHC 2.63158
4 1LT3 GAL BGC 2.91667
5 3S5W ONH 3.10078
6 4U8P UDP 3.48837
7 5W7B MYR 3.5461
8 4RYV ZEA 3.87097
9 2Q3M MLA 4.26357
10 6BR8 PGV 4.36508
11 2VMG MBG 4.4586
12 4NYT PC 4.60829
13 2C3H GLC GLC 5.10204
14 4UP4 GAL NAG 5.81395
15 4YDU ADP 6.97674
16 4RHS SIA SIA GAL 10.6557
17 2FPU HSO 13.0682
18 4DS0 A2G GAL NAG FUC 14.7239
19 1A5Z FBP 14.7287
20 5L2R MLA 18.9922
21 5Z84 CHD 28.2353
22 5W97 CHD 28.2353
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