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Receptor
PDB id Resolution Class Description Source Keywords
3DZI 1.73 Å EC: 3.2.2.5 CRYSTAL STRUCTURE OF HUMAN CD38 EXTRACELLULAR DOMAIN, RIBOSE-5'-PHOSPHATE INTERMEDIATE/GTP COMPLEX HOMO SAPIENS NONCOVALENT INTERMEDIATE GTP COMPLEX R5P-GTP ADDUCT BETA SHEETS ALPHA BUNDLE ALTERNATIVE SPLICING DIABETES MELLITUS GLYCOPROTEIN HYDROLASE MEMBRANE NAD POLYMORPHISM RECEPTOR SIGNAL-ANCHOR TRANSMEMBRANE
Ref.: COVALENT AND NONCOVALENT INTERMEDIATES OF AN NAD UTILIZING ENZYME, HUMAN CD38. CHEM.BIOL. V. 15 1068 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GTP B:302;
Valid;
none;
submit data
523.18 C10 H16 N5 O14 P3 c1nc2...
N B:301;
Invalid;
none;
submit data
214.11 C5 H11 O7 P C1[C@...
RGT A:301;
Valid;
none;
submit data
735.275 C15 H25 N5 O21 P4 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: GTP; Similar ligands found: 156
No: Ligand ECFP6 Tc MDL keys Tc
1 GTP 1 1
2 GP3 0.921053 0.973684
3 GDP 0.909091 1
4 GSP 0.853659 0.948718
5 GNH 0.82716 0.986667
6 G1R 0.819277 0.986667
7 GAV 0.811765 0.961039
8 9GM 0.809524 0.973684
9 GNP 0.809524 0.973684
10 GCP 0.797619 0.973684
11 5GP 0.797468 0.986486
12 G 0.797468 0.986486
13 GMV 0.764706 0.973684
14 G2R 0.764045 0.961039
15 G5P 0.755319 0.973684
16 GTG 0.752688 0.936709
17 G2P 0.747126 0.961039
18 G3A 0.744681 0.973684
19 GDD 0.741935 0.961039
20 GDC 0.741935 0.961039
21 GKE 0.741935 0.961039
22 0O2 0.736264 0.986486
23 GP2 0.729412 0.961039
24 6CK 0.726316 0.936709
25 Y9Z 0.723404 0.902439
26 GPG 0.717391 0.961039
27 GFB 0.715789 0.961039
28 GDR 0.715789 0.961039
29 GPD 0.704082 0.925
30 GKD 0.693878 0.961039
31 JB2 0.693878 0.961039
32 GDX 0.686869 0.973684
33 ALF 5GP 0.685393 0.888889
34 GH3 0.681319 0.973333
35 YGP 0.677083 0.901235
36 G3D 0.67033 0.986486
37 GDP AF3 0.659574 0.888889
38 ALF GDP 0.659574 0.888889
39 GDP ALF 0.659574 0.888889
40 DGT 0.659341 0.923077
41 GMP 0.658228 0.88
42 G4P 0.655914 0.986486
43 JB3 0.653846 0.948718
44 NGD 0.647619 0.961039
45 CAG 0.642202 0.880952
46 2MD 0.62963 0.891566
47 MGP 0.619565 0.961039
48 U2G 0.616822 0.936709
49 6G0 0.612903 0.961039
50 MGD 0.612613 0.891566
51 TPG 0.608696 0.840909
52 CG2 0.605505 0.936709
53 GDP 7MG 0.601942 0.911392
54 FEG 0.601852 0.879518
55 G G 0.598039 0.948052
56 ZGP 0.59633 0.869048
57 PGD 0.591304 0.925
58 MD1 0.591304 0.891566
59 3GP 0.590909 0.946667
60 GPX 0.581633 0.946667
61 DGI 0.580645 0.923077
62 IDP 0.576087 0.972973
63 DBG 0.567797 0.948718
64 2GP 0.555556 0.96
65 FE9 0.555556 0.776596
66 G4M 0.547619 0.880952
67 BGO 0.544643 0.924051
68 GCP G 0.543689 0.921053
69 ATP 0.537634 0.92
70 HEJ 0.537634 0.92
71 G1G 0.533898 0.925
72 AQP 0.531915 0.92
73 5FA 0.531915 0.92
74 A G 0.525862 0.935065
75 G A A A 0.525862 0.923077
76 U A G G 0.521368 0.935065
77 HFD 0.520833 0.873418
78 R5I 0.520408 0.946667
79 R7I 0.520408 0.946667
80 01G 0.518868 0.902439
81 P2G 0.510638 0.883117
82 ITT 0.510638 0.868421
83 AKW 0.504348 0.890244
84 GGM 0.504274 0.901235
85 G1R G1R 0.504065 0.924051
86 DGP 0.5 0.910256
87 PGD O 0.5 0.850575
88 MGO 0.5 0.864198
89 DG 0.5 0.910256
90 P1G 0.5 0.871795
91 GTA 0.495495 0.936709
92 PRT 0.490741 0.959459
93 B4P 0.489362 0.894737
94 AP5 0.489362 0.894737
95 IMP 0.489362 0.959459
96 G U 0.487179 0.9
97 7DT 0.484536 0.906667
98 GPC 0.479339 0.879518
99 G C 0.478992 0.9
100 BA3 0.478723 0.894737
101 ADP 0.473684 0.92
102 G2Q 0.471698 0.961039
103 6YZ 0.470588 0.896104
104 G7M 0.46875 0.948052
105 C1Z 0.462963 0.986486
106 25L 0.458716 0.907895
107 A2D 0.457447 0.894737
108 RGT 0.45045 0.909091
109 AGS 0.45 0.873418
110 SAP 0.45 0.873418
111 SGP 0.44898 0.82716
112 A4P 0.445378 0.869048
113 G G G RPC 0.442623 0.875
114 ANP 0.441176 0.896104
115 ACQ 0.441176 0.896104
116 8GT 0.441176 0.875
117 APC G U 0.44 0.886076
118 AT4 0.438776 0.884615
119 G U34 0.438017 0.888889
120 6AD 0.436893 0.841463
121 G G G C 0.433071 0.9125
122 UP5 0.432203 0.873418
123 PCG 0.431373 0.933333
124 C2E 0.431373 0.921053
125 35G 0.431373 0.933333
126 A G C C 0.429688 0.911392
127 T99 0.427184 0.884615
128 5GP 5GP 0.427184 0.883117
129 TAT 0.427184 0.884615
130 AR6 0.425743 0.894737
131 APR 0.425743 0.894737
132 7DD 0.424242 0.906667
133 AN2 0.424242 0.907895
134 DG DG 0.423423 0.865854
135 AD9 0.421569 0.896104
136 M33 0.42 0.883117
137 7D4 0.42 0.835443
138 UCG 0.419847 0.911392
139 HDV 0.419048 0.825
140 H6Y 0.419048 0.946667
141 G C C C 0.416667 0.924051
142 ACP 0.415842 0.896104
143 T5A 0.414634 0.802326
144 A1R 0.412844 0.839506
145 ADQ 0.412844 0.871795
146 MGQ 0.412844 0.935897
147 A3R 0.412844 0.839506
148 MGT 0.411215 0.823529
149 A G U 0.410072 0.888889
150 93A 0.41 0.833333
151 A22 0.407407 0.907895
152 CA0 0.405941 0.896104
153 ATF 0.40566 0.884615
154 AGO 0.404762 0.888889
155 MGV 0.401786 0.890244
156 CGP 0.4 0.86747
Ligand no: 2; Ligand: RGT; Similar ligands found: 78
No: Ligand ECFP6 Tc MDL keys Tc
1 RGT 1 1
2 HFD 0.585859 0.909091
3 ATP 0.571429 0.958904
4 HEJ 0.571429 0.958904
5 5FA 0.565657 0.958904
6 AQP 0.565657 0.958904
7 71V 0.546392 0.897436
8 G1R G1R 0.543307 0.911392
9 ITT 0.53 0.931507
10 B4P 0.525253 0.932432
11 ADP 0.525253 0.958904
12 AP5 0.525253 0.932432
13 BA3 0.515152 0.932432
14 6AD 0.514286 0.875
15 AGS 0.5 0.909091
16 SAP 0.5 0.909091
17 A2D 0.494949 0.932432
18 25L 0.491228 0.945946
19 6YZ 0.490741 0.933333
20 A 0.479592 0.931507
21 AMP 0.479592 0.931507
22 ANP 0.476636 0.933333
23 APR 0.47619 0.958904
24 AR6 0.47619 0.958904
25 ADQ 0.473214 0.933333
26 IMO 0.465347 0.917808
27 AVV 0.464286 0.8625
28 T99 0.462963 0.921053
29 ACQ 0.462963 0.933333
30 TAT 0.462963 0.921053
31 AT4 0.461538 0.921053
32 AN2 0.461538 0.945946
33 AD9 0.457944 0.933333
34 M33 0.457143 0.92
35 ACP 0.45283 0.933333
36 GTP 0.45045 0.909091
37 ADX 0.443396 0.841463
38 A22 0.442478 0.945946
39 ATF 0.441441 0.921053
40 25A 0.438596 0.932432
41 7RA 0.436893 0.945205
42 7DT 0.435185 0.945205
43 A3R 0.434783 0.873418
44 7D4 0.429907 0.87013
45 CA0 0.429907 0.933333
46 MGP 0.428571 0.875
47 HDV 0.428571 0.858974
48 9X8 0.42735 0.909091
49 OAD 0.42735 0.933333
50 50T 0.425926 0.92
51 6G0 0.424779 0.875
52 A1R 0.422414 0.873418
53 APC 0.422018 0.921053
54 PRX 0.422018 0.858974
55 PRT 0.421488 0.894737
56 3OD 0.420168 0.933333
57 AMZ 0.42 0.88
58 G5P 0.419355 0.910256
59 AFH 0.419355 0.875
60 N6P 0.418803 0.878378
61 UP5 0.417323 0.884615
62 GTA 0.416 0.876543
63 AIR 0.412371 0.864865
64 G3A 0.41129 0.910256
65 GDP 0.410714 0.909091
66 ABM 0.409524 0.881579
67 5AL 0.40708 0.92
68 C2R 0.405941 0.893333
69 PGS 0.40367 0.85
70 AU1 0.40367 0.933333
71 A12 0.401869 0.921053
72 AP2 0.401869 0.921053
73 6C6 0.401786 0.848101
74 GP3 0.401786 0.910256
75 OOB 0.401709 0.92
76 T5A 0.401515 0.811765
77 SRP 0.4 0.896104
78 MGO 0.4 0.829268
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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