Receptor
PDB id Resolution Class Description Source Keywords
2O3U 2.11 Å EC: 3.2.2.5 STRUCTURAL BASIS FOR FORMATION AND HYDROLYSIS OF CALCIUM MES CYCLIC ADP-RIBOSE BY HUMAN CD38 HOMO SAPIENS HUMAN CD38 E226Q MUTANT THE CATALYTIC POCKET NGD BINDING AHYDROLYSIS HYDROLASE
Ref.: STRUCTURAL BASIS FOR FORMATION AND HYDROLYSIS OF TH MESSENGER CYCLIC ADP-RIBOSE BY HUMAN CD38 J.BIOL.CHEM. V. 282 5853 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NGD A:301;
B:301;
Valid;
Valid;
none;
none;
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680.432 C21 H28 N7 O15 P2 c1cc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2PGJ 1.71 Å EC: 3.2.2.5 CATALYSIS ASSOCIATED CONFORMATIONAL CHANGES REVEALED BY HUMA COMPLEXED WITH A NON-HYDROLYZABLE SUBSTRATE ANALOG HOMO SAPIENS WILD-TYPE CD38 BOUND WITH N1-CIDPR THE CATALYTIC POCKET CONFORMATIONAL CHANGES OF THE ACTIVE SITE SUBSTRATE ANALOGHYDROLASE
Ref.: CATALYSIS-ASSOCIATED CONFORMATIONAL CHANGES REVEALE HUMAN CD38 COMPLEXED WITH A NON-HYDROLYZABLE SUBSTR ANALOG J.BIOL.CHEM. V. 282 24825 2007
Members (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2O3R - CXR C15 H21 N5 O13 P2 [H]/N=C/1c....
2 2O3U - NGD C21 H28 N7 O15 P2 c1cc(c[n+]....
3 2PGL - N1C C15 H20 N4 O14 P2 c1nc2c3n1[....
4 4OGW - NMN C11 H16 N2 O8 P c1cc(c[n+]....
5 3ROP - NCA C6 H6 N2 O c1cc(cnc1)....
6 3DZG - NCA C6 H6 N2 O c1cc(cnc1)....
7 2HCT - NMN C11 H16 N2 O8 P c1cc(c[n+]....
8 2I66 - G1R G1R n/a n/a
9 2O3S - CXR C15 H21 N5 O13 P2 [H]/N=C/1c....
10 3DZI - RGT C15 H25 N5 O21 P4 c1nc2c(n1[....
11 2I67 - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
12 3DZK - NMN C11 H16 N2 O8 P c1cc(c[n+]....
13 3DZH - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
14 4TMF - JS2 C14 H23 N5 O12 P2 C1=Nc2c(nc....
15 2PGJ ic50 = 0.26 mM N1C C15 H20 N4 O14 P2 c1nc2c3n1[....
16 3DZJ - NMN C11 H16 N2 O8 P c1cc(c[n+]....
17 2O3Q - CXR C15 H21 N5 O13 P2 [H]/N=C/1c....
18 2O3T - CGR C15 H23 N5 O14 P2 C1[C@@H]2[....
19 2I65 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
70% Homology Family (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2O3R - CXR C15 H21 N5 O13 P2 [H]/N=C/1c....
2 2O3U - NGD C21 H28 N7 O15 P2 c1cc(c[n+]....
3 2PGL - N1C C15 H20 N4 O14 P2 c1nc2c3n1[....
4 4OGW - NMN C11 H16 N2 O8 P c1cc(c[n+]....
5 3ROP - NCA C6 H6 N2 O c1cc(cnc1)....
6 3DZG - NCA C6 H6 N2 O c1cc(cnc1)....
7 2HCT - NMN C11 H16 N2 O8 P c1cc(c[n+]....
8 2I66 - G1R G1R n/a n/a
9 2O3S - CXR C15 H21 N5 O13 P2 [H]/N=C/1c....
10 3DZI - RGT C15 H25 N5 O21 P4 c1nc2c(n1[....
11 2I67 - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
12 3DZK - NMN C11 H16 N2 O8 P c1cc(c[n+]....
13 3DZH - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
14 4TMF - JS2 C14 H23 N5 O12 P2 C1=Nc2c(nc....
15 2PGJ ic50 = 0.26 mM N1C C15 H20 N4 O14 P2 c1nc2c3n1[....
16 3DZJ - NMN C11 H16 N2 O8 P c1cc(c[n+]....
17 2O3Q - CXR C15 H21 N5 O13 P2 [H]/N=C/1c....
18 2O3T - CGR C15 H23 N5 O14 P2 C1[C@@H]2[....
19 2I65 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2O3R - CXR C15 H21 N5 O13 P2 [H]/N=C/1c....
2 2O3U - NGD C21 H28 N7 O15 P2 c1cc(c[n+]....
3 2PGL - N1C C15 H20 N4 O14 P2 c1nc2c3n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; 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 GNP 0.62037 0.936709
12 GTG 0.617391 0.974684
13 G 0.601942 0.948052
14 5GP 0.601942 0.948052
15 GMV 0.601852 0.936709
16 GDX 0.583333 0.961538
17 GDC 0.581197 0.949367
18 GDD 0.581197 0.949367
19 GKE 0.581197 0.949367
20 GDR 0.576271 0.949367
21 GFB 0.576271 0.949367
22 GKD 0.575 0.949367
23 NAD 0.574803 0.922078
24 GP2 0.574074 0.925
25 JB3 0.572581 0.9375
26 G3A 0.571429 0.987013
27 6CK 0.571429 0.925926
28 GPD 0.570248 0.914634
29 G5P 0.566667 0.987013
30 GAV 0.566372 0.925
31 NFD 0.565891 0.876543
32 GDP MG 0.563636 0.9125
33 G2P 0.5625 0.925
34 NHD 0.5625 0.897436
35 JB2 0.561983 0.949367
36 NXX 0.560976 0.923077
37 DND 0.560976 0.923077
38 GPG 0.560345 0.974359
39 GDP BEF 0.558559 0.890244
40 GCP G 0.552632 0.924051
41 DBG 0.552239 0.962025
42 8ID 0.552 0.901235
43 NAJ 0.546875 0.922078
44 YGP 0.546219 0.891566
45 ALF 5GP 0.544643 0.879518
46 GTP MG 0.54386 0.9125
47 BEF GDP 0.54386 0.879518
48 2MD 0.542636 0.882353
49 MGD 0.541985 0.882353
50 FEG 0.53125 0.892857
51 CAG 0.530303 0.916667
52 GDP ALF 0.529915 0.879518
53 GDP AF3 0.529915 0.879518
54 G G 0.529412 0.974026
55 GDP 7MG 0.528455 0.949367
56 ZGP 0.527132 0.882353
57 CG2 0.523077 0.925926
58 NAD IBO 0.519084 0.864198
59 MD1 0.514706 0.882353
60 PGD 0.514706 0.914634
61 NMN 0.514563 0.831169
62 G3D 0.508621 0.948052
63 0O2 0.508333 0.948052
64 U2G 0.507692 0.925926
65 TPG 0.507246 0.833333
66 NAJ PYZ 0.5 0.845238
67 G4P 0.5 0.948052
68 A3D 0.496296 0.910256
69 GMP 0.495146 0.846154
70 NAP 0.485714 0.935065
71 FE9 0.485507 0.789474
72 GH3 0.478992 0.935897
73 NDO 0.478571 0.910256
74 I2C FE2 CMO CMO 0.471014 0.822222
75 3GP 0.468468 0.910256
76 G1G 0.467626 0.9625
77 CNA 0.466667 0.923077
78 BGO 0.462687 0.9375
79 NBP 0.458333 0.901235
80 U A G G 0.456522 0.974026
81 G4M 0.453333 0.894118
82 GGM 0.452555 0.914634
83 DGT 0.45 0.888889
84 GPX 0.447154 0.910256
85 MGP 0.445378 0.949367
86 6G0 0.441667 0.949367
87 DGI 0.440678 0.888889
88 G A A A 0.438849 0.961538
89 G1R G1R 0.434483 0.962025
90 AMP NAD 0.434483 0.875
91 PGD O 0.431507 0.863636
92 2GP 0.429825 0.923077
93 ZID 0.424658 0.935065
94 IDP 0.423729 0.935065
95 NNR 0.421569 0.705128
96 G C 0.421429 0.91358
97 GTA 0.421053 0.974684
98 G2Q 0.420635 0.925
99 NA0 0.418919 0.923077
100 NCN 0.414414 0.74359
101 GPC 0.412587 0.870588
102 TAP 0.412162 0.876543
103 G G G RPC 0.411348 0.9125
104 G G U 0.410448 0.974026
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 : 2PGJ; Ligand: N1C; Similar sites found: 3
This union binding pocket(no: 1) in the query (biounit: 2pgj.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4MUQ 2D8 0.01617 0.40452 1.96078
2 4MUQ LY0 0.02332 0.40047 1.96078
3 5MZI FAD 0.01494 0.41354 2.67176
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