Receptor
PDB id Resolution Class Description Source Keywords
1XJN 2.25 Å EC: 1.17.4.1 STRUCTURAL MECHANISM OF ALLOSTERIC SUBSTRATE SPECIFICITY IN RIBONUCLEOTIDE REDUCTASE: DATP-CDP COMPLEX THERMOTOGA MARITIMA RIBONUCLEOTIDE REDUCTASE 10 ALPHA-BETA BARREL ALLOSTERIC REGULATION SUBSTRATE SPECIFICITY PROTEIN-NUCLEOTIDE COMPLOXIDOREDUCTASE
Ref.: STRUCTURAL MECHANISM OF ALLOSTERIC SUBSTRATE SPECIF REGULATION IN A RIBONUCLEOTIDE REDUCTASE NAT.STRUCT.MOL.BIOL. V. 11 1142 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CDP A:1002;
B:1001;
C:1004;
D:1003;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 submit data
403.176 C9 H15 N3 O11 P2 C1=CN...
CL B:1009;
 Invalid;
 none;
 submit data
35.453 Cl [Cl-]
DTP A:1005;
B:1006;
C:1007;
C:1008;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 submit data
491.182 C10 H16 N5 O12 P3 c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3O0Q 1.8 Å EC: 1.17.4.1 THERMOTOGA MARITIMA RIBONUCLEOTIDE REDUCTASE, NRDJ, IN COMPL DTTP, GDP AND ADENOSINE THERMOTOGA MARITIMA 10 ALPHA/BETA BARREL ADENOSYLCOBALAMIN DEPENDENT RIBONUCLEREDUCTASE REDUCTION RIBONUCLEOTIDE 2-prime -OH POSITION EFFECTOSUBSTRATE GDP OXIDOREDUCTASE
Ref.: STRUCTURAL BASIS FOR ADENOSYLCOBALAMIN ACTIVATION I ADOCBL-DEPENDENT RIBONUCLEOTIDE REDUCTASES. ACS CHEM.BIOL. V. 5 933 2010
Members (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 1XJG - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
2 1XJJ - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
3 1XJN - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
4 1XJM - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
5 1XJF - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
6 1XJE - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
7 3O0N - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
8 3O0Q - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 3O0O - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
10 1XJK - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
70% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 1XJG - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
2 1XJJ - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
3 1XJN - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
4 1XJM - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
5 1XJF - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
6 1XJE - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
7 3O0N - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
8 3O0Q - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 3O0O - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
10 1XJK - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 1XJG - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
2 1XJJ - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
3 1XJN - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
4 1XJM - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
5 1XJF - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
6 1XJE - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
7 3O0N - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
8 3O0Q - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 3O0O - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
10 1XJK - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: CDP; Similar ligands found: 100
No: Ligand ECFP6 Tc MDL keys Tc
1 CDP 1 1
2 HF4 0.895522 1
3 CTP 0.895522 1
4 CAR 0.787879 0.985507
5 C 0.787879 0.985507
6 C5P 0.787879 0.985507
7 7XL 0.77027 0.944444
8 0RC 0.77027 0.918919
9 2TM 0.743243 0.958333
10 C2G 0.74026 0.957747
11 CDC 0.725 0.82716
12 CDP MG 0.722222 0.942857
13 C5G 0.707317 0.944444
14 CDM 0.695122 0.894737
15 CXY 0.678571 0.944444
16 AR3 0.636364 0.857143
17 CTN 0.636364 0.857143
18 1AA 0.619565 0.906667
19 A7R 0.606383 0.931507
20 UDP 0.605263 0.942029
21 I5A 0.602941 0.816901
22 YYY 0.582278 0.90411
23 CDP RB0 0.577778 0.917808
24 GCQ 0.560976 0.90411
25 C3P 0.56 0.942857
26 MCN 0.557692 0.819277
27 PMT 0.554455 0.85
28 91P 0.553398 0.851852
29 UTP 0.54321 0.942029
30 2AA 0.542857 0.693878
31 16B 0.538462 0.917808
32 CSV 0.536842 0.905405
33 CSQ 0.536842 0.905405
34 U5F 0.536585 0.942029
35 DCP 0.535714 0.90411
36 GTF 0.523256 0.90411
37 C2P 0.519481 0.957143
38 PCD 0.517857 0.781609
39 FZQ 0.511364 0.797619
40 FN5 0.509434 0.871795
41 GPC 0.509091 0.819277
42 CSF 0.504587 0.871795
43 DKZ 0.5 0.746667
44 NCC 0.495413 0.918919
45 HQ5 0.48913 0.758621
46 UNP 0.488372 0.915493
47 DCT 0.488372 0.90411
48 TKW 0.4875 0.971429
49 G G 6MZ C 0.486239 0.814815
50 G C 0.481818 0.8375
51 5GW 0.477778 0.890411
52 5HM 0.47561 0.958333
53 BUP 0.471264 0.878378
54 YSC 0.469388 0.767442
55 DCM 0.463415 0.890411
56 DC 0.463415 0.890411
57 UPP 0.451613 0.888889
58 UDH 0.451613 0.844156
59 G8D 0.450549 0.907895
60 U 0.45 0.927536
61 U5P 0.45 0.927536
62 C5P SIA 0.447368 0.893333
63 660 0.446809 0.876712
64 UFM 0.446809 0.888889
65 GDU 0.446809 0.888889
66 URM 0.446809 0.876712
67 UPG 0.446809 0.888889
68 8OD 0.445652 0.855263
69 0KX 0.444444 0.88
70 UPU 0.444444 0.887324
71 4GW 0.443299 0.866667
72 DOC 0.439024 0.890411
73 M7G 0.43617 0.829268
74 U2F 0.43299 0.842105
75 UFG 0.43299 0.842105
76 UPF 0.43299 0.842105
77 2KH 0.431818 0.915493
78 AWU 0.427083 0.888889
79 CG2 0.421053 0.873418
80 G3N 0.42 0.890411
81 UDP UDP 0.418605 0.885714
82 UDX 0.418367 0.888889
83 UAD 0.418367 0.888889
84 44P 0.416667 0.902778
85 3UC 0.415842 0.842105
86 DCP MG 0.413043 0.851351
87 M7M 0.412371 0.797619
88 8GT 0.410526 0.907895
89 V12 0.41 0.75
90 UGB 0.41 0.901408
91 UGA 0.41 0.901408
92 USQ 0.41 0.780488
93 UGF 0.405941 0.853333
94 UP5 0.405405 0.857143
95 GEO 0.405063 0.783784
96 UDM 0.403846 0.864865
97 H6Y 0.402062 0.855263
98 NVG 0.401961 0.731707
99 CTP C C C C 0.4 0.915493
100 6MZ C U 0.4 0.814815
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: CDP; Similar ligands found: 38
No: Ligand Similarity coefficient
1 DUD 0.9790
2 TBD 0.9634
3 TYD 0.9611
4 ADP 0.9333
5 D4D 0.9313
6 DUN 0.9274
7 ADX 0.9253
8 IDP 0.9252
9 BEF ADP 0.9235
10 AU1 0.9225
11 AN2 0.9215
12 ADP MG 0.9194
13 UMP 0.9193
14 AP2 0.9182
15 A12 0.9182
16 DGI 0.9158
17 M33 0.9122
18 CUU 0.9102
19 GDP 0.9093
20 AMP 0.9080
21 U3S 0.9071
22 DAT 0.9016
23 TMP 0.8942
24 U1S 0.8914
25 CH 0.8874
26 H2U 0.8816
27 2A5 0.8762
28 DU 0.8746
29 SON 0.8726
30 SSA 0.8707
31 AZD 0.8684
32 7D3 0.8672
33 T3S 0.8656
34 DDN 0.8643
35 DUT 0.8631
36 AMZ 0.8619
37 C8M 0.8613
38 BMP 0.8569
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 : 3O0Q; 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: 3o0q.bio1) has 61 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3O0Q; 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: 3o0q.bio1) has 57 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3O0Q; Ligand: TTP; 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: 3o0q.bio1) has 60 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3O0Q; Ligand: TTP; 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: 3o0q.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 3O0Q; Ligand: GDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 3o0q.bio1) has 61 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 3O0Q; Ligand: GDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 3o0q.bio1) has 57 residues
No: Leader PDB Ligand Sequence Similarity
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