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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: 144
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 GDC 0.734043 0.974026
15 GKE 0.734043 0.974026
16 GDD 0.734043 0.974026
17 Y9Z 0.734043 0.891566
18 GDR 0.726316 0.974026
19 GFB 0.726316 0.974026
20 GP2 0.72093 0.948718
21 6CK 0.71875 0.949367
22 GTG 0.708333 0.925
23 GKD 0.704082 0.974026
24 JB2 0.704082 0.974026
25 GAV 0.703297 0.948718
26 G3A 0.701031 0.961039
27 G2P 0.7 0.948718
28 GDX 0.69697 0.986842
29 GPD 0.69697 0.9375
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 ALF GDP 0.652632 0.878049
38 GDP AF3 0.652632 0.878049
39 GDP ALF 0.652632 0.878049
40 R5I 0.648352 0.96
41 R7I 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 PGD 0.6 0.91358
48 MD1 0.6 0.880952
49 G4P 0.597938 0.973333
50 FEG 0.59633 0.891566
51 U2G 0.59633 0.925
52 GDP 7MG 0.596154 0.9
53 G G 0.592233 0.935897
54 ZGP 0.590909 0.858824
55 G1R G1R 0.589744 0.936709
56 CG2 0.585586 0.925
57 TPG 0.576271 0.831461
58 3GP 0.566667 0.934211
59 DBG 0.563025 0.936709
60 GH3 0.555556 0.960526
61 G4M 0.555556 0.892857
62 FE9 0.550847 0.768421
63 APR 0.542553 0.907895
64 AR6 0.542553 0.907895
65 DGT 0.535354 0.911392
66 2GP 0.532609 0.947368
67 GPX 0.529412 0.934211
68 DGI 0.525773 0.911392
69 GCP G 0.52381 0.909091
70 A G 0.521368 0.923077
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 MGP 0.5 0.948718
76 BGO 0.5 0.936709
77 PGD O 0.496 0.840909
78 G2Q 0.495238 0.948718
79 6G0 0.49505 0.948718
80 P2G 0.489583 0.896104
81 GGM 0.487395 0.91358
82 AKW 0.487179 0.879518
83 P1G 0.479592 0.884615
84 DGP 0.479167 0.898734
85 DG 0.479167 0.898734
86 G U 0.470588 0.888889
87 IMP 0.46875 0.946667
88 A2D 0.468085 0.883117
89 GTA 0.464912 0.925
90 GPC 0.463415 0.869048
91 G C 0.46281 0.888889
92 5GP 5GP 0.45098 0.871795
93 G7M 0.44898 0.935897
94 BA3 0.443299 0.883117
95 G G G RPC 0.439024 0.864198
96 B4P 0.438776 0.883117
97 AP5 0.438776 0.883117
98 AT4 0.434343 0.873418
99 01G 0.433628 0.891566
100 ADV 0.431373 0.873418
101 RBY 0.431373 0.873418
102 M33 0.43 0.871795
103 SGP 0.43 0.817073
104 G G G C 0.429688 0.901235
105 35G 0.427184 0.921053
106 C2E 0.427184 0.909091
107 PCG 0.427184 0.921053
108 A G C C 0.426357 0.9
109 HEJ 0.425743 0.907895
110 ATP 0.425743 0.907895
111 APC G U 0.425197 0.875
112 ADP 0.424242 0.907895
113 ANP 0.423077 0.884615
114 A1R 0.422018 0.829268
115 AQP 0.421569 0.907895
116 5FA 0.421569 0.907895
117 A2R 0.420561 0.921053
118 AN2 0.42 0.896104
119 3OD 0.419643 0.909091
120 AGS 0.417476 0.8625
121 SAP 0.417476 0.8625
122 AD9 0.417476 0.884615
123 9X8 0.414414 0.8625
124 OAD 0.414414 0.909091
125 G C C C 0.413534 0.9125
126 HFD 0.413462 0.8625
127 AVV 0.412844 0.819277
128 AGO 0.412698 0.901235
129 ACP 0.411765 0.884615
130 G U34 0.41129 0.878049
131 MGO 0.411215 0.853659
132 ACQ 0.409524 0.884615
133 A3R 0.409091 0.829268
134 ADQ 0.409091 0.884615
135 MGQ 0.409091 0.924051
136 DG DG 0.40708 0.855422
137 A4P 0.406504 0.858824
138 UCG 0.406015 0.9
139 JBT 0.404624 0.789474
140 A22 0.40367 0.896104
141 CA0 0.401961 0.909091
142 ITT 0.401961 0.857143
143 ATF 0.401869 0.873418
144 ENP 0.401786 0.934211
Ligand no: 2; Ligand: G1R G1R; Similar ligands found: 71
No: Ligand ECFP6 Tc MDL keys Tc
1 G1R G1R 1 1
2 GDP ALF 0.591667 0.869048
3 GDP AF3 0.591667 0.869048
4 ALF GDP 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 G 0.525862 0.911392
11 5GP 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 GDC 0.515385 0.9375
19 GDD 0.515385 0.9375
20 GKE 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 U A G G 0.5 0.961538
29 GCP 0.5 0.901235
30 GDX 0.496296 0.949367
31 G2P 0.496 0.890244
32 GMV 0.491935 0.901235
33 GFB 0.488722 0.9375
34 GDR 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 NGD 0.434483 0.962025
53 FEG 0.434483 0.904762
54 3GP 0.434426 0.875
55 APC G U 0.433333 0.9125
56 G4P 0.431818 0.911392
57 ZGP 0.431507 0.872093
58 G C 0.425676 0.902439
59 MD1 0.424837 0.850575
60 U2G 0.424658 0.891566
61 ENQ 0.422222 0.871795
62 G4M 0.419753 0.905882
63 DBG 0.419355 0.925926
64 AR6 AR6 0.41844 0.897436
65 CAG 0.417219 0.883721
66 A G U 0.417178 0.914634
67 CG2 0.409396 0.891566
68 0O2 0.408759 0.911392
69 A G U U 0.404762 0.914634
70 FE9 0.4 0.762887
71 G G G C 0.4 0.914634
Ligand no: 3; Ligand: G2R; Similar ligands found: 120
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 9GM 0.747253 0.936709
9 GSP 0.747253 0.91358
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 GDR 0.666667 0.925
24 GFB 0.666667 0.925
25 GPG 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 JB2 0.647619 0.925
31 GKD 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 ALF GDP 0.613861 0.857143
38 GDP ALF 0.613861 0.857143
39 GDP AF3 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 FEG 0.578947 0.870588
45 CAG 0.576271 0.850575
46 G3D 0.574257 0.948052
47 G G 0.574074 0.9125
48 0O2 0.571429 0.948052
49 PGD 0.570248 0.891566
50 MD1 0.570248 0.882353
51 CG2 0.568965 0.902439
52 GDP 7MG 0.563636 0.878049
53 G4P 0.563107 0.948052
54 TPG 0.560976 0.813187
55 DBG 0.560976 0.91358
56 ZGP 0.560345 0.860465
57 GH3 0.553398 0.961039
58 AVV 0.553398 0.865854
59 FE9 0.536585 0.752577
60 DGT 0.533981 0.961538
61 3GP 0.53125 0.910256
62 DGI 0.524752 0.961538
63 G4M 0.518797 0.872093
64 R7I 0.514563 0.910256
65 R5I 0.514563 0.910256
66 GPX 0.514019 0.910256
67 A G 0.508197 0.9
68 U A G G 0.504065 0.9
69 2GP 0.5 0.923077
70 G A A A 0.495935 0.888889
71 GCP G 0.495495 0.886076
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 DG 0.48 0.948718
77 DGP 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 P1G 0.466019 0.8625
83 AKW 0.463415 0.858824
84 P2G 0.460784 0.85
85 G U 0.459677 0.86747
86 PCG 0.457143 0.897436
87 35G 0.457143 0.897436
88 C2E 0.457143 0.886076
89 GPC 0.453125 0.848837
90 NA7 0.442478 0.923077
91 GTA 0.441667 0.902439
92 IMP 0.441176 0.922078
93 G C 0.440945 0.86747
94 A2D 0.44 0.860759
95 5GP 5GP 0.439252 0.85
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 AT4 0.409524 0.851852
113 G C C C 0.405797 0.890244
114 SGP 0.40566 0.797619
115 HEJ 0.401869 0.884615
116 ATP 0.401869 0.884615
117 A3R 0.4 0.876543
118 ADP 0.4 0.884615
119 CGP 0.4 0.903614
120 A G U 0.4 0.857143
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: 45
This union binding pocket(no: 1) in the query (biounit: 2pgj.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 1HSL HIS 1.2605
2 4P7U 1PS 1.78571
3 3VOZ 04A 1.9084
4 4FFG 0U8 1.9084
5 4MUQ 2D8 1.96078
6 4MUQ LY0 1.96078
7 6BMM OLB 2.29008
8 5LX9 OLB 2.67176
9 3S5W ONH 2.67176
10 5MZI FAD 2.67176
11 5MZI FYK 2.67176
12 5Z3I ADE 2.67176
13 3MAN BMA BMA MAN 2.67176
14 5L2R MLA 3.05344
15 3TUR 6CL 3.05344
16 1L7P SEP 3.31754
17 2QES ADE 3.44828
18 5H4S RAM 3.81679
19 2WZF BGC 3.81679
20 1NU4 MLA 4.12371
21 4OJP MAL 4.19847
22 1TO9 HMH 4.23077
23 4CFT H4B 4.58015
24 4CU1 H4B 4.58015
25 1VAY AZA 4.58015
26 4RDN 6MD 4.79042
27 6CGN DA 4.96183
28 5VLQ ANP 4.96183
29 3ZPG 5GP 4.97382
30 5OCA 9QZ 5.06912
31 4MUS 2D8 5.21327
32 4MUS LY0 5.21327
33 2BVE PH5 5.34351
34 1M6P M6P 6.57895
35 1XPJ TLA 7.14286
36 1CY2 TMP 7.63359
37 2BO4 FLC 7.63359
38 4NOS H4B 8.01527
39 4NOS H2B 8.01527
40 2FPU HSO 8.52273
41 6BS6 GLC GLC GLC 9.54198
42 4CC6 L5Y 10.687
43 4OGQ 7PH 11.25
44 5W7B MYR 11.3475
45 3GCM 5GP 19.5122
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