Receptor
PDB id Resolution Class Description Source Keywords
2xjb 2.3 Å EC: 3.1.3.5 CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5'-NUCLEO II IN COMPLEX WITH DEOXYGUANOSINE MONOPHOSPHATE AND DEOXYADT RIPHOSPHATE HOMO SAPIENS ALLOSTERIC ENZYME CN-II GMP-IMP SPECIFIC NUCLEOTIDASE HIG5-PRIME NUCLEOTIDASE HYDROLASE METAL-BINDING NT5C2 NUCLMETABOLISM NUCLEOTIDE-BINDING PHOSPHOPROTEIN
Ref.: STRUCTURAL BASIS FOR THE ALLOSTERIC REGULATION AND SUBSTRATE RECOGNITION OF HUMAN CYTOSOLIC 5'-NUCLEOT J.MOL.BIOL. V. 408 684 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DG A:1491;
 Valid;
 none;
 submit data
347.221 C10 H14 N5 O7 P c1nc2...
DTP A:1490;
 Valid;
 none;
 submit data
491.182 C10 H16 N5 O12 P3 c1nc(...
GOL A:1489;
A:1492;
A:1493;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
MG A:1494;
A:1495;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2JC9 1.5 Å EC: 3.1.3.5 CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'-NUCLEOTIDASE II IN COMPLEX WITH ADENOSINE HOMO SAPIENS CYTOSOLIC 5-PRIME NUCLEOTIDASE II GMP-IMP SPECIFIC NUCLEOTIDASE CN-II NT5C2 HYDROLASE POLYMORPHISM CYTOSOLIC PURINE 5-PRIME NUCLEOTIDASE ALLOSTERIC ENZYME HIGH KM 5-PRIME NUCLEOTIDASE
Ref.: CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'-NUCLEOTIDASE II: INSIGHTS INTO ALLOSTERIC REGULATION AND SUBSTRATE RECOGNITION J.BIOL.CHEM. V. 282 17828 2007
Members (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 2JC9 - ADN C10 H13 N5 O4 c1nc(c2c(n....
2 2XJF - DG2 C3 H8 O10 P2 C([C@H](C(....
3 2XJE - U5P C9 H13 N2 O9 P C1=CN(C(=O....
4 2XCV - IMP C10 H13 N4 O8 P c1nc2c(n1[....
5 2XJD - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
6 6DE2 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
7 2XCW - IMP C10 H13 N4 O8 P c1nc2c(n1[....
8 2XJC - B4P C20 H28 N10 O19 P4 c1nc(c2c(n....
9 6DDZ - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
10 2XJB - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
70% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 2JC9 - ADN C10 H13 N5 O4 c1nc(c2c(n....
2 2XJF - DG2 C3 H8 O10 P2 C([C@H](C(....
3 2XJE - U5P C9 H13 N2 O9 P C1=CN(C(=O....
4 2XCV - IMP C10 H13 N4 O8 P c1nc2c(n1[....
5 2XJD - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
6 6DE2 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
7 2XCW - IMP C10 H13 N4 O8 P c1nc2c(n1[....
8 2XJC - B4P C20 H28 N10 O19 P4 c1nc(c2c(n....
9 6DDZ - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
10 2XJB - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
11 5OPK - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
12 5OPM - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
50% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 2JC9 - ADN C10 H13 N5 O4 c1nc(c2c(n....
2 2XJF - DG2 C3 H8 O10 P2 C([C@H](C(....
3 2XJE - U5P C9 H13 N2 O9 P C1=CN(C(=O....
4 2XCV - IMP C10 H13 N4 O8 P c1nc2c(n1[....
5 2XJD - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
6 6DE2 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
7 2XCW - IMP C10 H13 N4 O8 P c1nc2c(n1[....
8 2XJC - B4P C20 H28 N10 O19 P4 c1nc(c2c(n....
9 6DDZ - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
10 2XJB - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
11 5OPK - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
12 5OPM - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: DG; Similar ligands found: 78
No: Ligand ECFP6 Tc MDL keys Tc
1 DGP 1 1
2 DG 1 1
3 DGI 0.815789 0.986842
4 DGT 0.775 0.986842
5 DI 0.62963 0.973333
6 5GP 0.60241 0.922078
7 G 0.60241 0.922078
8 CGP 0.596154 0.925926
9 GDP 0.516484 0.910256
10 GH3 0.515789 0.935065
11 DA 0.511905 0.894737
12 D5M 0.511905 0.894737
13 3GP 0.505747 0.909091
14 2GP 0.505747 0.922078
15 GP3 0.505495 0.8875
16 G3D 0.505263 0.922078
17 GTP 0.5 0.910256
18 GP2 0.5 0.924051
19 G4P 0.494845 0.922078
20 GNH 0.494624 0.898734
21 P2G 0.494382 0.871795
22 G2P 0.489583 0.924051
23 GMP 0.487805 0.797468
24 GMV 0.484211 0.8875
25 ALF 5GP 0.484211 0.833333
26 P1G 0.483516 0.884615
27 G2R 0.48 0.948718
28 GAV 0.479592 0.876543
29 GCP 0.479167 0.911392
30 G1R 0.479167 0.898734
31 6OG 0.477778 0.886076
32 0O2 0.475248 0.922078
33 GSP 0.474227 0.865854
34 9GM 0.474227 0.8875
35 GNP 0.474227 0.8875
36 3PD UM3 0.473214 0.878049
37 DOI 0.47191 0.87013
38 6MA 0.47191 0.858974
39 GDP BEF 0.463918 0.875
40 GPG 0.460784 0.876543
41 GPX 0.46 0.909091
42 GTP MG 0.459184 0.897436
43 GDP ALF 0.455446 0.833333
44 3ZE 0.451613 0.897436
45 CF2 0.451613 0.811765
46 GPD 0.449541 0.890244
47 GDC 0.443396 0.876543
48 GKE 0.443396 0.876543
49 Y9Z 0.443396 0.869048
50 GDD 0.443396 0.876543
51 GDP AF3 0.441176 0.833333
52 G3A 0.435185 0.8875
53 YGP 0.433962 0.845238
54 KB7 0.43299 0.795181
55 G5P 0.431193 0.8875
56 SGP 0.430108 0.817073
57 JB2 0.427273 0.876543
58 GTG 0.425926 0.855422
59 GFB 0.425926 0.876543
60 GDR 0.425926 0.876543
61 DAT 0.425532 0.896104
62 6CK 0.422018 0.855422
63 DZ4 0.418367 0.873418
64 GKD 0.414414 0.876543
65 DU DU DU DU BRU DG DU 0.414062 0.827586
66 BGO 0.413793 0.865854
67 U2G 0.413793 0.855422
68 GDX 0.410714 0.8875
69 DTP 0.408163 0.896104
70 CG2 0.40678 0.855422
71 AS 0.406593 0.85
72 KBD 0.40566 0.795181
73 GDP 7MG 0.405405 0.853659
74 JB3 0.405172 0.865854
75 UCG 0.404762 0.876543
76 8OG 0.404255 0.855422
77 FEG 0.401709 0.869048
78 NGD 0.401709 0.876543
Ligand no: 2; Ligand: DTP; Similar ligands found: 187
No: Ligand ECFP6 Tc MDL keys Tc
1 DTP 1 1
2 DAT 0.891892 1
3 DA 0.773333 0.971831
4 D5M 0.773333 0.971831
5 DZ4 0.705882 0.972603
6 AS 0.696203 0.92
7 DDS 0.694118 0.944444
8 HF7 0.689655 0.986111
9 3AT 0.655172 0.931507
10 7D4 0.635294 0.893333
11 ATP 0.627907 0.905405
12 HEJ 0.627907 0.905405
13 3D1 0.626667 0.835616
14 3L1 0.626667 0.835616
15 AQP 0.62069 0.905405
16 5FA 0.62069 0.905405
17 CPA 0.584906 0.8625
18 ZDA 0.577778 0.853333
19 B4P 0.574713 0.88
20 AP5 0.574713 0.88
21 CUU 0.573034 0.931507
22 5F1 0.56962 0.794521
23 BA3 0.563218 0.88
24 DGT 0.557895 0.909091
25 ADP 0.556818 0.905405
26 101 0.552941 0.917808
27 7D3 0.551724 0.893333
28 A2D 0.54023 0.88
29 6MA 0.539326 0.931507
30 DOI 0.539326 0.917808
31 2A5 0.532609 0.932432
32 6YZ 0.53125 0.906667
33 25L 0.529412 0.893333
34 PAP 0.526882 0.917808
35 AGS 0.526882 0.858974
36 ATR 0.526882 0.930556
37 T99 0.515789 0.87013
38 TAT 0.515789 0.87013
39 103 0.505747 0.826667
40 AN2 0.5 0.893333
41 AT4 0.5 0.87013
42 APR 0.5 0.88
43 AR6 0.5 0.88
44 ACQ 0.5 0.906667
45 A3R 0.49505 0.921053
46 A1R 0.49505 0.921053
47 AD9 0.494737 0.881579
48 M33 0.494624 0.868421
49 AV2 0.489796 0.88
50 ACP 0.489362 0.906667
51 A 0.488636 0.878378
52 AMP 0.488636 0.878378
53 7D5 0.488372 0.866667
54 T5A 0.486957 0.853659
55 NA7 0.485437 0.945946
56 DGI 0.484536 0.909091
57 ANP 0.484536 0.881579
58 128 0.482143 0.747126
59 HQG 0.48 0.893333
60 A2R 0.48 0.893333
61 CA0 0.478723 0.857143
62 ADX 0.478723 0.795181
63 A22 0.475248 0.893333
64 HDV 0.474747 0.881579
65 JSQ 0.474227 0.858974
66 HFD 0.474227 0.858974
67 KG4 0.473684 0.857143
68 45A 0.472527 0.831169
69 ABM 0.472527 0.831169
70 PRX 0.46875 0.833333
71 APC 0.46875 0.92
72 ADQ 0.466019 0.857143
73 PPS 0.464646 0.817073
74 ITT 0.463158 0.853333
75 6OG 0.463158 0.907895
76 A3P 0.462366 0.90411
77 A2P 0.462366 0.916667
78 ATF 0.46 0.87013
79 50T 0.458333 0.868421
80 N5P 0.456311 0.797468
81 4AD 0.451923 0.883117
82 AMP MG 0.450549 0.84
83 8LE 0.45 0.8125
84 5AL 0.45 0.844156
85 3OD 0.448598 0.857143
86 JNT 0.447619 0.906667
87 A12 0.446809 0.92
88 AP2 0.446809 0.92
89 QA7 0.446602 0.8125
90 G5P 0.446429 0.8375
91 A4P 0.444444 0.790698
92 UP5 0.443478 0.835443
93 OAD 0.443396 0.857143
94 9X8 0.443396 0.835443
95 MDR 0.44186 0.783784
96 SRP 0.441176 0.87013
97 8LH 0.441176 0.822785
98 7DT 0.438776 0.891892
99 ADP BEF 0.4375 0.853333
100 ADP MG 0.4375 0.853333
101 G3A 0.4375 0.8375
102 AP0 0.435897 0.814815
103 NB8 0.435185 0.860759
104 SRA 0.434783 0.833333
105 APC MG 0.434343 0.855263
106 DLL 0.433962 0.844156
107 00A 0.433962 0.802469
108 2AM 0.433333 0.90411
109 AU1 0.43299 0.881579
110 DCP 0.43299 0.831169
111 8LQ 0.432692 0.846154
112 6V0 0.431034 0.814815
113 NAI 0.431034 0.825
114 GTA 0.429825 0.807229
115 3AM 0.428571 0.864865
116 OOB 0.428571 0.844156
117 8QN 0.428571 0.844156
118 OZV 0.428571 0.88
119 5SV 0.428571 0.814815
120 25A 0.428571 0.88
121 9SN 0.427273 0.792683
122 WAQ 0.425926 0.871795
123 PR8 0.425926 0.8625
124 V3L 0.425743 0.88
125 NDP 0.425 0.8375
126 139 0.425 0.8625
127 AMO 0.424528 0.894737
128 PAJ 0.424528 0.804878
129 KMQ 0.423423 0.846154
130 PTJ 0.422018 0.814815
131 FYA 0.422018 0.893333
132 1ZZ 0.422018 0.807229
133 BIS 0.422018 0.848101
134 NZQ 0.421488 0.85
135 ADV 0.42 0.894737
136 ADP PO3 0.42 0.853333
137 ATP MG 0.42 0.853333
138 RBY 0.42 0.894737
139 OVE 0.419355 0.868421
140 MAP 0.419048 0.858974
141 GGZ 0.419048 0.792683
142 TXD 0.418803 0.848101
143 3AD 0.418605 0.77027
144 VO4 ADP 0.417476 0.857143
145 ALF ADP 0.417476 0.790123
146 ANP MG 0.417476 0.844156
147 KF5 0.416667 0.635135
148 3UK 0.416667 0.833333
149 BEF ADP 0.415842 0.831169
150 TXE 0.415254 0.848101
151 0WD 0.414634 0.8375
152 12D 0.413793 0.755814
153 LAD 0.412844 0.85
154 B5V 0.412844 0.822785
155 GAP 0.411765 0.810127
156 2FD 0.411111 0.805195
157 FA5 0.410714 0.87013
158 48N 0.410256 0.8375
159 CNA 0.409836 0.87013
160 TXP 0.409836 0.860759
161 PUA 0.409449 0.897436
162 TXA 0.409091 0.846154
163 ME8 0.409091 0.807229
164 AFH 0.408696 0.82716
165 DGP 0.408163 0.896104
166 SON 0.408163 0.894737
167 DG 0.408163 0.896104
168 V2G 0.407767 0.860759
169 AHX 0.407407 0.860759
170 NAX 0.40678 0.839506
171 DND 0.40678 0.846154
172 NJP 0.406504 0.858974
173 DAL AMP 0.40566 0.820513
174 DQV 0.405172 0.868421
175 7D7 0.404762 0.733333
176 OMR 0.403361 0.819277
177 GH3 0.401869 0.858974
178 LAQ 0.401709 0.807229
179 NPW 0.401639 0.851852
180 ADS THS THS THS 0.401575 0.770115
181 XYA 0.4 0.76
182 RAB 0.4 0.76
183 F6G 0.4 0.797468
184 CL9 0.4 0.805195
185 J4G 0.4 0.883117
186 L3W 0.4 0.846154
187 ADN 0.4 0.76
Similar Ligands (3D)
Ligand no: 1; Ligand: DG; Similar ligands found: 130
No: Ligand Similarity coefficient
1 IMU 0.9717
2 XMP 0.9715
3 71V 0.9688
4 AMP 0.9620
5 G7M 0.9564
6 IMP 0.9534
7 IRP 0.9460
8 AMP MG 0.9432
9 BRU 0.9428
10 TMP 0.9399
11 5CM 0.9389
12 8BR 0.9361
13 6CG 0.9338
14 UFP 0.9327
15 FMP 0.9326
16 93A 0.9293
17 6MZ 0.9276
18 EO7 0.9226
19 FDM 0.9223
20 JLN 0.9218
21 5IU 0.9217
22 8OP 0.9208
23 5HU 0.9197
24 PCG 0.9192
25 8GM 0.9185
26 7D5 0.9173
27 45A 0.9160
28 ZAS 0.9159
29 UMP 0.9149
30 U5P 0.9142
31 QBT 0.9139
32 LMS 0.9131
33 AOC 0.9120
34 5FU 0.9112
35 Z8B 0.9109
36 CNU 0.9109
37 5BU 0.9107
38 ABM 0.9093
39 NMN 0.9085
40 9L3 0.9061
41 C2R 0.9054
42 MTA 0.9052
43 DCM 0.9027
44 A3N 0.9016
45 4X2 0.9011
46 C 0.8994
47 GNG 0.8993
48 SRA 0.8992
49 BMQ 0.8988
50 PFU 0.8986
51 5HM 0.8982
52 N5O 0.8980
53 NYM 0.8978
54 NEC 0.8965
55 AMZ 0.8964
56 CL9 0.8958
57 NIA 0.8956
58 DU 0.8948
59 MCF 0.8947
60 6RE 0.8940
61 J7C 0.8940
62 2DT 0.8935
63 DUS 0.8931
64 TKW 0.8930
65 BMP 0.8920
66 NWQ 0.8906
67 C5P 0.8904
68 35G 0.8903
69 SSI 0.8902
70 EP4 0.8900
71 BVP 0.8897
72 D4M 0.8896
73 H2U 0.8886
74 2FA 0.8880
75 UP6 0.8877
76 3DH 0.8869
77 8HG 0.8867
78 FNU 0.8863
79 NCN 0.8859
80 O8M 0.8833
81 6U5 0.8821
82 U 0.8810
83 13A 0.8799
84 100 0.8795
85 DSH 0.8791
86 16B 0.8791
87 CA0 0.8785
88 SNP 0.8778
89 103 0.8774
90 581 0.8765
91 43H 0.8762
92 3Q1 0.8762
93 3D1 0.8761
94 ATM 0.8761
95 MG7 0.8759
96 4UO 0.8756
97 KG4 0.8754
98 JFX 0.8752
99 ADP 0.8750
100 DDN 0.8731
101 PWH 0.8722
102 ADN 0.8717
103 A4D 0.8714
104 5CD 0.8713
105 3F5 0.8713
106 TZY 0.8709
107 UMC 0.8694
108 DC 0.8690
109 PRX 0.8686
110 FMC 0.8685
111 M33 0.8681
112 CAR 0.8676
113 M7G 0.8667
114 NWW 0.8659
115 5N5 0.8657
116 TXS 0.8650
117 PRH 0.8648
118 ADX 0.8645
119 RVP 0.8642
120 NOS 0.8625
121 T21 0.8605
122 75G 0.8599
123 A3P 0.8587
124 0JB 0.8583
125 A3S 0.8581
126 FN5 0.8574
127 JP3 0.8566
128 M8Q 0.8562
129 101 0.8557
130 ZX8 0.8508
Ligand no: 2; Ligand: DTP; Similar ligands found: 32
No: Ligand Similarity coefficient
1 TTP 0.9873
2 GNP 0.9719
3 GTP 0.9699
4 GSP 0.9655
5 GDP BEF 0.9613
6 BEF GDP 0.9585
7 GCP 0.9553
8 GDP AF3 0.9521
9 DUT 0.9505
10 9GM 0.9499
11 ALF GDP 0.9474
12 GDP ALF 0.9469
13 DBG 0.9381
14 ADP ALF 0.9354
15 UTP 0.9313
16 CTP 0.9261
17 HF4 0.9191
18 ADP AF3 0.9091
19 GDP MG 0.8952
20 MGT 0.8868
21 SSA 0.8856
22 GNH 0.8843
23 GDP 0.8842
24 GTF 0.8819
25 DSZ 0.8793
26 SAM 0.8779
27 Y9Z 0.8743
28 D3T 0.8721
29 2KH 0.8700
30 A5A 0.8669
31 SAH 0.8653
32 IDP 0.8579
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2JC9; Ligand: ADN; 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: 2jc9.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2JC9; Ligand: ADN; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2jc9.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2JC9; Ligand: ADN; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 2jc9.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2JC9; Ligand: ADN; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 2jc9.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
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