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 (2D)
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 9GM 0.77907 0.961039
10 GNP 0.77907 0.961039
11 G 0.765432 0.973333
12 5GP 0.765432 0.973333
13 GMV 0.755814 0.961039
14 GDD 0.734043 0.974026
15 GDC 0.734043 0.974026
16 Y9Z 0.734043 0.891566
17 GKE 0.734043 0.974026
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 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 GDX 0.69697 0.986842
29 GPD 0.69697 0.9375
30 G5P 0.693878 0.961039
31 GPG 0.691489 0.948718
32 GDP BEF 0.688889 0.923077
33 GTP MG 0.681319 0.947368
34 ALF 5GP 0.677778 0.878049
35 YGP 0.670103 0.890244
36 JB3 0.663462 0.961538
37 NGD 0.657143 0.948718
38 2MD 0.654206 0.880952
39 GDP ALF 0.652632 0.878049
40 GDP AF3 0.652632 0.878049
41 R7I 0.648352 0.96
42 R5I 0.648352 0.96
43 MGD 0.636364 0.880952
44 GMP 0.62963 0.868421
45 G3D 0.610526 0.973333
46 CAG 0.607143 0.870588
47 0O2 0.606061 0.973333
48 KB7 0.602151 0.839506
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 KBD 0.574257 0.839506
60 3GP 0.566667 0.934211
61 DBG 0.563025 0.936709
62 GH3 0.555556 0.960526
63 G4M 0.555556 0.892857
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 IDP 0.520833 0.96
73 QBQ 0.520408 0.973333
74 I2C FE2 CMO CMO 0.512397 0.8
75 G1G 0.504132 0.91358
76 BGO 0.5 0.936709
77 MGP 0.5 0.948718
78 PGD O 0.496 0.840909
79 G2Q 0.495238 0.948718
80 6G0 0.49505 0.948718
81 P2G 0.489583 0.896104
82 GGM 0.487395 0.91358
83 AKW 0.487179 0.879518
84 P1G 0.479592 0.884615
85 DGP 0.479167 0.898734
86 DG 0.479167 0.898734
87 IMP 0.46875 0.946667
88 A2D 0.468085 0.883117
89 CZF 0.465347 0.921053
90 GTA 0.464912 0.925
91 GPC 0.463415 0.869048
92 G C 0.46281 0.888889
93 5GP 5GP 0.45098 0.871795
94 G7M 0.44898 0.935897
95 BA3 0.443299 0.883117
96 AP5 0.438776 0.883117
97 B4P 0.438776 0.883117
98 AT4 0.434343 0.873418
99 01G 0.433628 0.891566
100 RBY 0.431373 0.873418
101 ADV 0.431373 0.873418
102 SGP 0.43 0.817073
103 M33 0.43 0.871795
104 PCG 0.427184 0.921053
105 C2E 0.427184 0.909091
106 35G 0.427184 0.921053
107 APC G U 0.426357 0.875
108 ATP 0.425743 0.907895
109 HEJ 0.425743 0.907895
110 GZ0 0.425 0.961538
111 ADP 0.424242 0.907895
112 ANP 0.423077 0.884615
113 A1R 0.422018 0.829268
114 5FA 0.421569 0.907895
115 AQP 0.421569 0.907895
116 A2R 0.420561 0.921053
117 AN2 0.42 0.896104
118 3OD 0.419643 0.909091
119 AD9 0.417476 0.884615
120 AGS 0.417476 0.8625
121 9X8 0.414414 0.8625
122 OAD 0.414414 0.909091
123 JSQ 0.413462 0.8625
124 HFD 0.413462 0.8625
125 AVV 0.412844 0.819277
126 AGO 0.412698 0.901235
127 ACP 0.411765 0.884615
128 MGO 0.411215 0.853659
129 ACQ 0.409524 0.884615
130 A3R 0.409091 0.829268
131 ADQ 0.409091 0.884615
132 MGQ 0.409091 0.924051
133 HQG 0.407407 0.921053
134 A4P 0.406504 0.858824
135 UCG 0.406015 0.9
136 JNT 0.405405 0.860759
137 JBT 0.404624 0.789474
138 A22 0.40367 0.896104
139 M7G A2M G 0.402597 0.8
140 CA0 0.401961 0.909091
141 ITT 0.401961 0.857143
142 ATF 0.401869 0.873418
143 ENP 0.401786 0.934211
144 NYZ 0.4 0.924051
Ligand no: 2; Ligand: G1R G1R; Similar ligands found: 70
No: Ligand ECFP6 Tc MDL keys Tc
1 G1R G1R 1 1
2 GDP BEF 0.617391 0.9125
3 GTP MG 0.612069 0.935897
4 GDP ALF 0.591667 0.869048
5 GDP AF3 0.591667 0.869048
6 G1R 0.589744 0.936709
7 GDP 7MG 0.5625 0.9375
8 ALF 5GP 0.554622 0.869048
9 RGT 0.543307 0.911392
10 GDP 0.542373 0.924051
11 5GP 0.525862 0.911392
12 G 0.525862 0.911392
13 GNH 0.525 0.9125
14 PGD O 0.524138 0.833333
15 GP3 0.521008 0.949367
16 GNP 0.520325 0.901235
17 9GM 0.520325 0.901235
18 GDD 0.515385 0.9375
19 GDC 0.515385 0.9375
20 GKE 0.515385 0.9375
21 GSP 0.508065 0.879518
22 G3A 0.507576 0.949367
23 GP2 0.504132 0.890244
24 GTP 0.504065 0.924051
25 G5P 0.503759 0.949367
26 GCP 0.5 0.901235
27 GDX 0.496296 0.949367
28 G2P 0.496 0.890244
29 GMV 0.491935 0.901235
30 GDR 0.488722 0.9375
31 GFB 0.488722 0.9375
32 G2R 0.488372 0.890244
33 GAV 0.488189 0.890244
34 6CK 0.485075 0.914634
35 JB2 0.477941 0.9375
36 I2C FE2 CMO CMO 0.47619 0.813187
37 Y9Z 0.470149 0.83908
38 JB3 0.468085 0.925926
39 GKD 0.467153 0.9375
40 GTG 0.466667 0.938272
41 2MD 0.465278 0.850575
42 GPD 0.463768 0.903614
43 GPG 0.462121 0.9375
44 YGP 0.451852 0.858824
45 G3D 0.449612 0.911392
46 MGD 0.445946 0.850575
47 M7G A2M G 0.445087 0.833333
48 GMP 0.443478 0.835443
49 KB7 0.440945 0.809524
50 FEG 0.434483 0.904762
51 NGD 0.434483 0.962025
52 3GP 0.434426 0.875
53 APC G U 0.434211 0.9125
54 G4P 0.431818 0.911392
55 ZGP 0.431507 0.872093
56 KBD 0.42963 0.853659
57 G C 0.425676 0.902439
58 MD1 0.424837 0.850575
59 U2G 0.424658 0.891566
60 ENQ 0.422222 0.871795
61 G4M 0.419753 0.905882
62 DBG 0.419355 0.925926
63 AR6 AR6 0.41844 0.897436
64 KBJ 0.417266 0.823529
65 CAG 0.417219 0.883721
66 BEF ADP 0.414062 0.85
67 CG2 0.409396 0.891566
68 0O2 0.408759 0.911392
69 VO4 ADP 0.40458 0.851852
70 FE9 0.4 0.762887
Ligand no: 3; Ligand: G2R; Similar ligands found: 116
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 9GM 0.747253 0.936709
8 GNP 0.747253 0.936709
9 GSP 0.747253 0.91358
10 GCP 0.736264 0.961538
11 5GP 0.712644 0.948052
12 G 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 GDD 0.673267 0.925
19 GDC 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 GDR 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 GDP BEF 0.645833 0.9
34 GDX 0.641509 0.936709
35 GTP MG 0.639175 0.923077
36 ALF 5GP 0.635417 0.857143
37 YGP 0.631068 0.869048
38 JB3 0.627273 0.91358
39 GDP ALF 0.613861 0.857143
40 GDP AF3 0.613861 0.857143
41 2MD 0.605263 0.860465
42 U2G 0.59292 0.902439
43 MGD 0.589744 0.860465
44 GMP 0.586207 0.846154
45 KB7 0.581633 0.819277
46 FEG 0.578947 0.870588
47 CAG 0.576271 0.850575
48 G3D 0.574257 0.948052
49 0O2 0.571429 0.948052
50 MD1 0.570248 0.882353
51 PGD 0.570248 0.891566
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 I2C FE2 CMO CMO 0.5 0.782609
71 2GP 0.5 0.923077
72 QBQ 0.490385 0.948052
73 IDP 0.490196 0.935065
74 G1R G1R 0.488372 0.890244
75 BGO 0.487603 0.890244
76 G1G 0.480315 0.891566
77 DGP 0.48 0.948718
78 DG 0.48 0.948718
79 GGM 0.475806 0.869048
80 PGD O 0.473282 0.822222
81 MGP 0.471698 0.925
82 6G0 0.46729 0.925
83 P1G 0.466019 0.8625
84 AKW 0.463415 0.858824
85 P2G 0.460784 0.85
86 PCG 0.457143 0.897436
87 C2E 0.457143 0.886076
88 35G 0.457143 0.897436
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 CZF 0.439252 0.897436
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 UCG 0.419118 0.878049
102 APC G U 0.41791 0.876543
103 BA3 0.417476 0.860759
104 B4P 0.413462 0.860759
105 AP5 0.413462 0.860759
106 ANP 0.412844 0.8625
107 01G 0.411765 0.915663
108 AT4 0.409524 0.851852
109 SGP 0.40566 0.797619
110 M7G A2M G 0.405063 0.782609
111 GZ0 0.404762 0.9375
112 HEJ 0.401869 0.884615
113 ATP 0.401869 0.884615
114 CGP 0.4 0.903614
115 ADP 0.4 0.884615
116 A3R 0.4 0.876543
Similar Ligands (3D)
Ligand no: 1; Ligand: G1R; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; Ligand: G1R G1R; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 3; Ligand: G2R; 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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