Receptor
PDB id Resolution Class Description Source Keywords
2I66 1.7 Å EC: 3.2.2.5 STRUCTURAL BASIS FOR THE MECHANISTIC UNDERSTANDING HUMAN CD38 CONTROLLED MULTIPLE CATALYSIS HOMO SAPIENS THE CATALYTIC POCKET REACTION PRODUCT REACTION INTERMEDIATE HYDROLASE
Ref.: STRUCTURAL BASIS FOR THE MECHANISTIC UNDERSTANDING OF HUMAN CD38-CONTROLLED MULTIPLE CATALYSIS. J.BIOL.CHEM. V. 281 32861 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
G1R B:301;
Valid;
none;
submit data
575.315 C15 H23 N5 O15 P2 c1nc2...
G1R G1R A:301;
Valid;
none;
submit data
1128.59 n/a [P+](...
G2R B:302;
Valid;
none;
submit data
559.316 C15 H23 N5 O14 P2 c1nc2...
View in 3D viewer
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 (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: G1R; Similar ligands found: 139
No: Ligand ECFP6 Tc MDL keys Tc
1 G1R 1 1
2 GP3 0.860759 0.961039
3 GDP 0.82716 0.986667
4 GTP 0.819277 0.986667
5 GNH 0.817073 0.973684
6 GSP 0.8 0.936709
7 G2R 0.795455 0.948718
8 GCP 0.788235 0.961039
9 GNP 0.77907 0.961039
10 5GP 0.765432 0.973333
11 G 0.765432 0.973333
12 GMV 0.755814 0.961039
13 GDD 0.734043 0.974026
14 Y9Z 0.734043 0.891566
15 GKE 0.734043 0.974026
16 GDC 0.734043 0.974026
17 GFB 0.726316 0.974026
18 GDR 0.726316 0.974026
19 GP2 0.72093 0.948718
20 6CK 0.71875 0.949367
21 GTG 0.708333 0.925
22 GDP MG 0.704545 0.911392
23 JB2 0.704082 0.974026
24 GKD 0.704082 0.974026
25 GAV 0.703297 0.948718
26 G3A 0.701031 0.961039
27 G2P 0.7 0.948718
28 GPD 0.69697 0.9375
29 GDX 0.69697 0.986842
30 GDP BEF 0.696629 0.888889
31 G5P 0.693878 0.961039
32 BEF GDP 0.692308 0.878049
33 GPG 0.691489 0.948718
34 ALF 5GP 0.677778 0.878049
35 GTP MG 0.673913 0.911392
36 YGP 0.670103 0.890244
37 GCP G 0.666667 0.923077
38 JB3 0.663462 0.961538
39 NGD 0.657143 0.948718
40 2MD 0.654206 0.880952
41 GDP ALF 0.652632 0.878049
42 GDP AF3 0.652632 0.878049
43 MGD 0.636364 0.880952
44 GMP 0.62963 0.868421
45 G G 0.616162 0.923077
46 G3D 0.610526 0.973333
47 CAG 0.607143 0.870588
48 0O2 0.606061 0.973333
49 MD1 0.6 0.880952
50 PGD 0.6 0.91358
51 G4P 0.597938 0.973333
52 FEG 0.59633 0.891566
53 U2G 0.59633 0.925
54 GDP 7MG 0.596154 0.9
55 ZGP 0.590909 0.858824
56 G1R G1R 0.589744 0.936709
57 CG2 0.585586 0.925
58 TPG 0.576271 0.831461
59 3GP 0.566667 0.934211
60 DBG 0.563025 0.936709
61 GH3 0.555556 0.960526
62 G4M 0.555556 0.892857
63 FE9 0.550847 0.768421
64 AR6 0.542553 0.907895
65 APR 0.542553 0.907895
66 DGT 0.535354 0.911392
67 I2C FE2 CMO CMO 0.533898 0.8
68 2GP 0.532609 0.947368
69 GPX 0.529412 0.934211
70 DGI 0.525773 0.911392
71 IDP 0.520833 0.96
72 U A G G 0.516949 0.923077
73 G A A A 0.508475 0.911392
74 G1G 0.504132 0.91358
75 BGO 0.5 0.936709
76 MGP 0.5 0.948718
77 PGD O 0.496 0.840909
78 G2Q 0.495238 0.948718
79 6G0 0.49505 0.948718
80 G G U 0.491071 0.923077
81 P2G 0.489583 0.896104
82 GGM 0.487395 0.91358
83 P1G 0.479592 0.884615
84 DGP 0.479167 0.898734
85 DG 0.479167 0.898734
86 IMP 0.46875 0.946667
87 A2D 0.468085 0.883117
88 GTA 0.464912 0.925
89 GPC 0.463415 0.869048
90 G C 0.46281 0.888889
91 5GP 5GP 0.45098 0.871795
92 G7M 0.44898 0.935897
93 BA3 0.443299 0.883117
94 G G G RPC 0.439024 0.864198
95 AP5 0.438776 0.883117
96 B4P 0.438776 0.883117
97 U G A 0.434783 0.878049
98 01G 0.433628 0.891566
99 ADV 0.431373 0.873418
100 RBY 0.431373 0.873418
101 M33 0.43 0.871795
102 SGP 0.43 0.817073
103 G G G C 0.429688 0.901235
104 C2E 0.427184 0.909091
105 PCG 0.427184 0.921053
106 35G 0.427184 0.921053
107 A G C C 0.426357 0.9
108 ATP 0.425743 0.907895
109 APC G U 0.425197 0.875
110 ADP 0.424242 0.907895
111 ANP 0.423077 0.884615
112 A1R 0.422018 0.829268
113 AQP 0.421569 0.907895
114 5FA 0.421569 0.907895
115 A2R 0.420561 0.921053
116 AN2 0.42 0.896104
117 3OD 0.419643 0.909091
118 SAP 0.417476 0.8625
119 AGS 0.417476 0.8625
120 AD9 0.417476 0.884615
121 OAD 0.414414 0.909091
122 G C C C 0.413534 0.9125
123 AVV 0.412844 0.819277
124 AGO 0.412698 0.901235
125 ACP 0.411765 0.884615
126 G U34 0.41129 0.878049
127 MGO 0.411215 0.853659
128 ACQ 0.409524 0.884615
129 ADQ 0.409091 0.884615
130 MGQ 0.409091 0.924051
131 DG DG 0.40708 0.855422
132 A4P 0.406504 0.858824
133 UCG 0.406015 0.9
134 JBT 0.404624 0.789474
135 A22 0.40367 0.896104
136 CA0 0.401961 0.909091
137 ITT 0.401961 0.857143
138 ATF 0.401869 0.873418
139 ENP 0.401786 0.934211
Ligand no: 2; Ligand: G1R G1R; Similar ligands found: 75
No: Ligand ECFP6 Tc MDL keys Tc
1 G1R G1R 1 1
2 GDP MG 0.628319 0.901235
3 GTP MG 0.62069 0.901235
4 GDP BEF 0.608696 0.879518
5 BEF GDP 0.606838 0.869048
6 GDP AF3 0.591667 0.869048
7 GDP ALF 0.591667 0.869048
8 G1R 0.589744 0.936709
9 GDP 7MG 0.5625 0.9375
10 ALF 5GP 0.554622 0.869048
11 RGT 0.543307 0.911392
12 GDP 0.542373 0.924051
13 G G 0.527559 0.961538
14 G 0.525862 0.911392
15 5GP 0.525862 0.911392
16 GNH 0.525 0.9125
17 PGD O 0.524138 0.833333
18 GP3 0.521008 0.949367
19 GNP 0.520325 0.901235
20 GDC 0.515385 0.9375
21 GDD 0.515385 0.9375
22 GKE 0.515385 0.9375
23 G A A A 0.514286 0.949367
24 GCP G 0.512 0.9125
25 GSP 0.508065 0.879518
26 G3A 0.507576 0.949367
27 GP2 0.504132 0.890244
28 GTP 0.504065 0.924051
29 G5P 0.503759 0.949367
30 GCP 0.5 0.901235
31 U A G G 0.5 0.961538
32 GDX 0.496296 0.949367
33 G2P 0.496 0.890244
34 GMV 0.491935 0.901235
35 GDR 0.488722 0.9375
36 GFB 0.488722 0.9375
37 G2R 0.488372 0.890244
38 GAV 0.488189 0.890244
39 6CK 0.485075 0.914634
40 JB2 0.477941 0.9375
41 I2C FE2 CMO CMO 0.472603 0.813187
42 Y9Z 0.470149 0.83908
43 JB3 0.468085 0.925926
44 GKD 0.467153 0.9375
45 GTG 0.466667 0.938272
46 2MD 0.465278 0.850575
47 GPD 0.463768 0.903614
48 GPG 0.462121 0.9375
49 YGP 0.451852 0.858824
50 U G A 0.45 0.914634
51 G3D 0.449612 0.911392
52 MGD 0.445946 0.850575
53 GMP 0.443478 0.835443
54 G G U 0.435714 0.936709
55 NGD 0.434483 0.962025
56 FEG 0.434483 0.904762
57 3GP 0.434426 0.875
58 APC G U 0.433333 0.9125
59 G4P 0.431818 0.911392
60 ZGP 0.431507 0.872093
61 G C 0.425676 0.902439
62 MD1 0.424837 0.850575
63 U2G 0.424658 0.891566
64 ENQ 0.422222 0.871795
65 G4M 0.419753 0.905882
66 DBG 0.419355 0.925926
67 AR6 AR6 0.41844 0.897436
68 CAG 0.417219 0.883721
69 A G U 0.417178 0.914634
70 CG2 0.409396 0.891566
71 0O2 0.408759 0.911392
72 ADP MG 0.404762 0.839506
73 ATP MG 0.403101 0.839506
74 FE9 0.4 0.762887
75 G G G C 0.4 0.914634
Ligand no: 3; Ligand: G2R; Similar ligands found: 117
No: Ligand ECFP6 Tc MDL keys Tc
1 G2R 1 1
2 GP3 0.8 0.936709
3 G1R 0.795455 0.948718
4 GDP 0.770115 0.961039
5 GTP 0.764045 0.961039
6 GNH 0.761364 0.948718
7 GNP 0.747253 0.936709
8 GSP 0.747253 0.91358
9 GCP 0.736264 0.961538
10 5GP 0.712644 0.948052
11 G 0.712644 0.948052
12 Y9Z 0.707071 0.892857
13 GMV 0.706522 0.936709
14 6CK 0.676471 0.902439
15 GP2 0.673913 0.974359
16 G2P 0.673684 0.974359
17 GDD 0.673267 0.925
18 GKE 0.673267 0.925
19 GDC 0.673267 0.925
20 GPD 0.673077 0.914634
21 GFB 0.666667 0.925
22 GTG 0.666667 0.902439
23 GPG 0.666667 0.925
24 GDR 0.666667 0.925
25 G3A 0.660194 0.936709
26 GAV 0.659794 0.925
27 GDP MG 0.659574 0.888889
28 G5P 0.653846 0.936709
29 GDP BEF 0.652632 0.86747
30 NGD 0.651376 0.925
31 BEF GDP 0.649485 0.857143
32 GKD 0.647619 0.925
33 JB2 0.647619 0.925
34 G2Q 0.646465 1
35 GDX 0.641509 0.936709
36 ALF 5GP 0.635417 0.857143
37 GTP MG 0.632653 0.888889
38 YGP 0.631068 0.869048
39 JB3 0.627273 0.91358
40 GCP G 0.626263 0.9
41 GDP AF3 0.613861 0.857143
42 GDP ALF 0.613861 0.857143
43 2MD 0.605263 0.860465
44 G G 0.596154 0.9
45 U2G 0.59292 0.902439
46 MGD 0.589744 0.860465
47 GMP 0.586207 0.846154
48 FEG 0.578947 0.870588
49 CAG 0.576271 0.850575
50 G3D 0.574257 0.948052
51 0O2 0.571429 0.948052
52 MD1 0.570248 0.882353
53 PGD 0.570248 0.891566
54 CG2 0.568965 0.902439
55 GDP 7MG 0.563636 0.878049
56 G4P 0.563107 0.948052
57 TPG 0.560976 0.813187
58 DBG 0.560976 0.91358
59 ZGP 0.560345 0.860465
60 AVV 0.553398 0.865854
61 GH3 0.553398 0.961039
62 I2C FE2 CMO CMO 0.545455 0.782609
63 FE9 0.536585 0.752577
64 DGT 0.533981 0.961538
65 3GP 0.53125 0.910256
66 DGI 0.524752 0.961538
67 G4M 0.518797 0.872093
68 GPX 0.514019 0.910256
69 U A G G 0.504065 0.9
70 2GP 0.5 0.923077
71 G A A A 0.495935 0.888889
72 IDP 0.490196 0.935065
73 G1R G1R 0.488372 0.890244
74 BGO 0.487603 0.890244
75 G1G 0.480315 0.891566
76 DGP 0.48 0.948718
77 DG 0.48 0.948718
78 GGM 0.475806 0.869048
79 PGD O 0.473282 0.822222
80 MGP 0.471698 0.925
81 6G0 0.46729 0.925
82 G G U 0.466102 0.9
83 P1G 0.466019 0.8625
84 P2G 0.460784 0.85
85 C2E 0.457143 0.886076
86 PCG 0.457143 0.897436
87 35G 0.457143 0.897436
88 GPC 0.453125 0.848837
89 NA7 0.442478 0.923077
90 GTA 0.441667 0.902439
91 IMP 0.441176 0.922078
92 G C 0.440945 0.86747
93 A2D 0.44 0.860759
94 5GP 5GP 0.439252 0.85
95 U G A 0.43662 0.857143
96 G G G RPC 0.429688 0.843373
97 A1R 0.424779 0.876543
98 APR 0.424528 0.860759
99 AR6 0.424528 0.860759
100 G7M 0.423077 0.9125
101 G G G C 0.421053 0.879518
102 UCG 0.419118 0.878049
103 A G C C 0.41791 0.878049
104 BA3 0.417476 0.860759
105 APC G U 0.416667 0.876543
106 G U34 0.414062 0.857143
107 B4P 0.413462 0.860759
108 AP5 0.413462 0.860759
109 ANP 0.412844 0.8625
110 01G 0.411765 0.915663
111 DG DG 0.410256 0.902439
112 G C C C 0.405797 0.890244
113 SGP 0.40566 0.797619
114 ATP 0.401869 0.884615
115 A G U 0.4 0.857143
116 CGP 0.4 0.903614
117 ADP 0.4 0.884615
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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