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 (2D)
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 9GM 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 GDD 0.581197 0.949367
20 GDC 0.581197 0.949367
21 GDR 0.576271 0.949367
22 GFB 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 6CK 0.571429 0.925926
28 G3A 0.571429 0.987013
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 GPG 0.560345 0.974359
38 GDP BEF 0.553571 0.924051
39 DBG 0.552239 0.962025
40 8ID 0.552 0.901235
41 GTP MG 0.548673 0.948052
42 NAJ 0.546875 0.922078
43 YGP 0.546219 0.891566
44 ALF 5GP 0.544643 0.879518
45 2MD 0.542636 0.882353
46 MGD 0.541985 0.882353
47 NAD IBO 0.539683 0.909091
48 NAD TDB 0.539683 0.909091
49 A7R 0.532787 0.8625
50 FEG 0.53125 0.892857
51 CAG 0.530303 0.916667
52 GDP AF3 0.529915 0.879518
53 GDP ALF 0.529915 0.879518
54 GDP 7MG 0.528455 0.949367
55 ZGP 0.527132 0.882353
56 CG2 0.523077 0.925926
57 MD1 0.514706 0.882353
58 PGD 0.514706 0.914634
59 NMN 0.514563 0.831169
60 KB7 0.513274 0.797619
61 G3D 0.508621 0.948052
62 KBD 0.508333 0.841463
63 0O2 0.508333 0.948052
64 U2G 0.507692 0.925926
65 TPG 0.507246 0.833333
66 G4P 0.5 0.948052
67 A3D 0.496296 0.910256
68 GMP 0.495146 0.846154
69 KBJ 0.491935 0.811765
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 3GP 0.468468 0.910256
75 G1G 0.467626 0.9625
76 CNA 0.466667 0.923077
77 BGO 0.462687 0.9375
78 QBQ 0.461538 0.948052
79 AMP NAD 0.459854 0.897436
80 NBP 0.458333 0.901235
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 I2C FE2 CMO CMO 0.443662 0.822222
87 6G0 0.441667 0.949367
88 DGI 0.440678 0.888889
89 G1R G1R 0.434483 0.962025
90 R7I 0.433333 0.910256
91 R5I 0.433333 0.910256
92 PGD O 0.431507 0.863636
93 AKW 0.430657 0.926829
94 2GP 0.429825 0.923077
95 ZID 0.424658 0.935065
96 IDP 0.423729 0.935065
97 NNR 0.421569 0.705128
98 G C 0.421429 0.91358
99 GTA 0.421053 0.974684
100 G2Q 0.420635 0.925
101 NA0 0.418919 0.923077
102 9JJ 0.417178 0.879518
103 NCN 0.414414 0.74359
104 GPC 0.412587 0.870588
105 TAP 0.412162 0.876543
106 N01 0.409722 0.897436
107 NAQ 0.408163 0.888889
108 DG 0.401709 0.876543
109 G7M 0.401709 0.936709
110 DGP 0.401709 0.876543
111 NAE 0.401361 0.911392
Similar Ligands (3D)
Ligand no: 1; Ligand: NGD; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2PGJ; Ligand: N1C; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2pgj.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
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