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(=O)...
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: 149
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 9GM 0.77907 0.961039
11 5GP 0.765432 0.973333
12 G 0.765432 0.973333
13 GMV 0.755814 0.961039
14 GDD 0.734043 0.974026
15 GKE 0.734043 0.974026
16 Y9Z 0.734043 0.891566
17 GDC 0.734043 0.974026
18 GFB 0.726316 0.974026
19 GDR 0.726316 0.974026
20 GP2 0.72093 0.948718
21 6CK 0.71875 0.949367
22 GTG 0.708333 0.925
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 G5P 0.693878 0.961039
31 GPG 0.691489 0.948718
32 ALF 5GP 0.677778 0.878049
33 YGP 0.670103 0.890244
34 JB3 0.663462 0.961538
35 NGD 0.657143 0.948718
36 2MD 0.654206 0.880952
37 GDP AF3 0.652632 0.878049
38 ALF GDP 0.652632 0.878049
39 GDP ALF 0.652632 0.878049
40 R7I 0.648352 0.96
41 R5I 0.648352 0.96
42 MGD 0.636364 0.880952
43 GMP 0.62963 0.868421
44 G3D 0.610526 0.973333
45 CAG 0.607143 0.870588
46 0O2 0.606061 0.973333
47 KB7 0.602151 0.839506
48 MD1 0.6 0.880952
49 PGD 0.6 0.91358
50 G4P 0.597938 0.973333
51 U2G 0.59633 0.925
52 FEG 0.59633 0.891566
53 GDP 7MG 0.596154 0.9
54 G G 0.592233 0.935897
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 KBD 0.574257 0.839506
60 3GP 0.566667 0.934211
61 DBG 0.563025 0.936709
62 G4M 0.555556 0.892857
63 GH3 0.555556 0.960526
64 KBJ 0.552381 0.809524
65 FE9 0.550847 0.768421
66 APR 0.542553 0.907895
67 AR6 0.542553 0.907895
68 DGT 0.535354 0.911392
69 2GP 0.532609 0.947368
70 GPX 0.529412 0.934211
71 DGI 0.525773 0.911392
72 GCP G 0.52381 0.909091
73 A G 0.521368 0.923077
74 IDP 0.520833 0.96
75 U A G G 0.516949 0.923077
76 G A A A 0.508475 0.911392
77 G1G 0.504132 0.91358
78 BGO 0.5 0.936709
79 MGP 0.5 0.948718
80 PGD O 0.496 0.840909
81 G2Q 0.495238 0.948718
82 6G0 0.49505 0.948718
83 P2G 0.489583 0.896104
84 GGM 0.487395 0.91358
85 AKW 0.487179 0.879518
86 P1G 0.479592 0.884615
87 DG 0.479167 0.898734
88 DGP 0.479167 0.898734
89 G U 0.470588 0.888889
90 IMP 0.46875 0.946667
91 A2D 0.468085 0.883117
92 GTA 0.464912 0.925
93 GPC 0.463415 0.869048
94 G C 0.46281 0.888889
95 5GP 5GP 0.45098 0.871795
96 G7M 0.44898 0.935897
97 BA3 0.443299 0.883117
98 G G G RPC 0.439024 0.864198
99 AP5 0.438776 0.883117
100 B4P 0.438776 0.883117
101 AT4 0.434343 0.873418
102 01G 0.433628 0.891566
103 RBY 0.431373 0.873418
104 ADV 0.431373 0.873418
105 M33 0.43 0.871795
106 SGP 0.43 0.817073
107 G G G C 0.429688 0.901235
108 PCG 0.427184 0.921053
109 C2E 0.427184 0.909091
110 35G 0.427184 0.921053
111 A G C C 0.426357 0.9
112 ATP 0.425743 0.907895
113 HEJ 0.425743 0.907895
114 APC G U 0.425197 0.875
115 ADP 0.424242 0.907895
116 ANP 0.423077 0.884615
117 A1R 0.422018 0.829268
118 AQP 0.421569 0.907895
119 5FA 0.421569 0.907895
120 A2R 0.420561 0.921053
121 AN2 0.42 0.896104
122 3OD 0.419643 0.909091
123 AD9 0.417476 0.884615
124 SAP 0.417476 0.8625
125 AGS 0.417476 0.8625
126 OAD 0.414414 0.909091
127 9X8 0.414414 0.8625
128 G C C C 0.413534 0.9125
129 JSQ 0.413462 0.8625
130 HFD 0.413462 0.8625
131 AVV 0.412844 0.819277
132 AGO 0.412698 0.901235
133 ACP 0.411765 0.884615
134 G U34 0.41129 0.878049
135 MGO 0.411215 0.853659
136 ACQ 0.409524 0.884615
137 MGQ 0.409091 0.924051
138 ADQ 0.409091 0.884615
139 A3R 0.409091 0.829268
140 HQG 0.407407 0.921053
141 DG DG 0.40708 0.855422
142 A4P 0.406504 0.858824
143 UCG 0.406015 0.9
144 JBT 0.404624 0.789474
145 A22 0.40367 0.896104
146 CA0 0.401961 0.909091
147 ITT 0.401961 0.857143
148 ATF 0.401869 0.873418
149 ENP 0.401786 0.934211
Ligand no: 2; Ligand: G1R G1R; Similar ligands found: 74
No: Ligand ECFP6 Tc MDL keys Tc
1 G1R G1R 1 1
2 GDP AF3 0.591667 0.869048
3 ALF GDP 0.591667 0.869048
4 GDP ALF 0.591667 0.869048
5 G1R 0.589744 0.936709
6 GDP 7MG 0.5625 0.9375
7 ALF 5GP 0.554622 0.869048
8 RGT 0.543307 0.911392
9 GDP 0.542373 0.924051
10 5GP 0.525862 0.911392
11 G 0.525862 0.911392
12 GNH 0.525 0.9125
13 PGD O 0.524138 0.833333
14 G G 0.523077 0.949367
15 GP3 0.521008 0.949367
16 9GM 0.520325 0.901235
17 GNP 0.520325 0.901235
18 GKE 0.515385 0.9375
19 GDC 0.515385 0.9375
20 GDD 0.515385 0.9375
21 G A A A 0.514286 0.949367
22 GSP 0.508065 0.879518
23 G3A 0.507576 0.949367
24 GP2 0.504132 0.890244
25 GTP 0.504065 0.924051
26 G5P 0.503759 0.949367
27 A G 0.503546 0.961538
28 GCP 0.5 0.901235
29 U A G G 0.5 0.961538
30 GDX 0.496296 0.949367
31 G2P 0.496 0.890244
32 GMV 0.491935 0.901235
33 GDR 0.488722 0.9375
34 GFB 0.488722 0.9375
35 G2R 0.488372 0.890244
36 GAV 0.488189 0.890244
37 6CK 0.485075 0.914634
38 JB2 0.477941 0.9375
39 Y9Z 0.470149 0.83908
40 JB3 0.468085 0.925926
41 GKD 0.467153 0.9375
42 GTG 0.466667 0.938272
43 2MD 0.465278 0.850575
44 GPD 0.463768 0.903614
45 GPG 0.462121 0.9375
46 GCP G 0.458647 0.898734
47 YGP 0.451852 0.858824
48 G3D 0.449612 0.911392
49 MGD 0.445946 0.850575
50 GMP 0.443478 0.835443
51 G U 0.441379 0.902439
52 KB7 0.440945 0.809524
53 FEG 0.434483 0.904762
54 NGD 0.434483 0.962025
55 3GP 0.434426 0.875
56 APC G U 0.433333 0.9125
57 G4P 0.431818 0.911392
58 ZGP 0.431507 0.872093
59 KBD 0.42963 0.853659
60 G C 0.425676 0.902439
61 MD1 0.424837 0.850575
62 U2G 0.424658 0.891566
63 ENQ 0.422222 0.871795
64 G4M 0.419753 0.905882
65 DBG 0.419355 0.925926
66 AR6 AR6 0.41844 0.897436
67 KBJ 0.417266 0.823529
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 A G U U 0.404762 0.914634
73 G G G C 0.4 0.914634
74 FE9 0.4 0.762887
Ligand no: 3; Ligand: G2R; Similar ligands found: 123
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 GSP 0.747253 0.91358
8 9GM 0.747253 0.936709
9 GNP 0.747253 0.936709
10 GCP 0.736264 0.961538
11 G 0.712644 0.948052
12 5GP 0.712644 0.948052
13 Y9Z 0.707071 0.892857
14 GMV 0.706522 0.936709
15 6CK 0.676471 0.902439
16 GP2 0.673913 0.974359
17 G2P 0.673684 0.974359
18 GDC 0.673267 0.925
19 GDD 0.673267 0.925
20 GKE 0.673267 0.925
21 GPD 0.673077 0.914634
22 GTG 0.666667 0.902439
23 GFB 0.666667 0.925
24 GPG 0.666667 0.925
25 GDR 0.666667 0.925
26 G3A 0.660194 0.936709
27 GAV 0.659794 0.925
28 G5P 0.653846 0.936709
29 NGD 0.651376 0.925
30 GKD 0.647619 0.925
31 JB2 0.647619 0.925
32 G2Q 0.646465 1
33 GDX 0.641509 0.936709
34 ALF 5GP 0.635417 0.857143
35 YGP 0.631068 0.869048
36 JB3 0.627273 0.91358
37 GDP AF3 0.613861 0.857143
38 ALF GDP 0.613861 0.857143
39 GDP ALF 0.613861 0.857143
40 2MD 0.605263 0.860465
41 U2G 0.59292 0.902439
42 MGD 0.589744 0.860465
43 GMP 0.586207 0.846154
44 KB7 0.581633 0.819277
45 FEG 0.578947 0.870588
46 CAG 0.576271 0.850575
47 G3D 0.574257 0.948052
48 G G 0.574074 0.9125
49 0O2 0.571429 0.948052
50 PGD 0.570248 0.891566
51 MD1 0.570248 0.882353
52 CG2 0.568965 0.902439
53 GDP 7MG 0.563636 0.878049
54 G4P 0.563107 0.948052
55 DBG 0.560976 0.91358
56 TPG 0.560976 0.813187
57 ZGP 0.560345 0.860465
58 GH3 0.553398 0.961039
59 AVV 0.553398 0.865854
60 KBD 0.542056 0.819277
61 FE9 0.536585 0.752577
62 DGT 0.533981 0.961538
63 3GP 0.53125 0.910256
64 DGI 0.524752 0.961538
65 KBJ 0.522523 0.811765
66 G4M 0.518797 0.872093
67 R7I 0.514563 0.910256
68 R5I 0.514563 0.910256
69 GPX 0.514019 0.910256
70 A G 0.508197 0.9
71 U A G G 0.504065 0.9
72 2GP 0.5 0.923077
73 G A A A 0.495935 0.888889
74 GCP G 0.495495 0.886076
75 IDP 0.490196 0.935065
76 G1R G1R 0.488372 0.890244
77 BGO 0.487603 0.890244
78 G1G 0.480315 0.891566
79 DG 0.48 0.948718
80 DGP 0.48 0.948718
81 GGM 0.475806 0.869048
82 PGD O 0.473282 0.822222
83 MGP 0.471698 0.925
84 6G0 0.46729 0.925
85 P1G 0.466019 0.8625
86 AKW 0.463415 0.858824
87 P2G 0.460784 0.85
88 G U 0.459677 0.86747
89 35G 0.457143 0.897436
90 PCG 0.457143 0.897436
91 C2E 0.457143 0.886076
92 GPC 0.453125 0.848837
93 NA7 0.442478 0.923077
94 GTA 0.441667 0.902439
95 IMP 0.441176 0.922078
96 G C 0.440945 0.86747
97 A2D 0.44 0.860759
98 5GP 5GP 0.439252 0.85
99 G G G RPC 0.429688 0.843373
100 A1R 0.424779 0.876543
101 APR 0.424528 0.860759
102 AR6 0.424528 0.860759
103 G7M 0.423077 0.9125
104 G G G C 0.421053 0.879518
105 UCG 0.419118 0.878049
106 A G C C 0.41791 0.878049
107 BA3 0.417476 0.860759
108 APC G U 0.416667 0.876543
109 G U34 0.414062 0.857143
110 AP5 0.413462 0.860759
111 B4P 0.413462 0.860759
112 ANP 0.412844 0.8625
113 01G 0.411765 0.915663
114 DG DG 0.410256 0.902439
115 AT4 0.409524 0.851852
116 G C C C 0.405797 0.890244
117 SGP 0.40566 0.797619
118 ATP 0.401869 0.884615
119 HEJ 0.401869 0.884615
120 A3R 0.4 0.876543
121 A G U 0.4 0.857143
122 ADP 0.4 0.884615
123 CGP 0.4 0.903614
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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