Receptor
PDB id Resolution Class Description Source Keywords
1XJG 2.5 Å EC: 1.17.4.1 STRUCTURAL MECHANISM OF ALLOSTERIC SUBSTRATE SPECIFICITY IN RIBONUCLEOTIDE REDUCTASE: DATP-UDP 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
DTP A:1004;
B:1003;
 Valid;
Valid;
 none;
none;
 submit data
491.182 C10 H16 N5 O12 P3 c1nc(...
MG A:1006;
B:1005;
 Invalid;
Invalid;
 none;
none;
 submit data
24.305 Mg [Mg+2...
UDP A:1001;
B:1002;
 Valid;
Valid;
 none;
none;
 submit data
404.161 C9 H14 N2 O12 P2 C1=CN...
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: 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
Ligand no: 2; Ligand: UDP; Similar ligands found: 123
No: Ligand ECFP6 Tc MDL keys Tc
1 UDP 1 1
2 UTP 0.892308 1
3 U5F 0.878788 1
4 UNP 0.8 0.970149
5 U5P 0.78125 0.984615
6 U 0.78125 0.984615
7 UPU 0.72973 0.940298
8 2KH 0.722222 0.970149
9 44P 0.720588 0.955882
10 UFM 0.717949 0.941176
11 URM 0.717949 0.927536
12 660 0.717949 0.927536
13 UPG 0.717949 0.941176
14 GDU 0.717949 0.941176
15 UDP UDP 0.714286 0.939394
16 UDH 0.705128 0.864865
17 UPP 0.705128 0.941176
18 UFG 0.691358 0.888889
19 U2F 0.691358 0.888889
20 UPF 0.691358 0.888889
21 AWU 0.6875 0.941176
22 UAD 0.670732 0.941176
23 UDX 0.670732 0.941176
24 3UC 0.658824 0.888889
25 UGA 0.654762 0.955224
26 UGB 0.654762 0.955224
27 USQ 0.654762 0.820513
28 G3N 0.647059 0.914286
29 UGF 0.647059 0.901408
30 UDM 0.636364 0.914286
31 URI 0.625 0.863636
32 UD1 0.622222 0.927536
33 UD2 0.622222 0.927536
34 UDP GAL 0.611765 0.913043
35 Y6W 0.607143 0.888889
36 CDP 0.605263 0.942029
37 HP7 0.591398 0.941176
38 UD7 0.591398 0.927536
39 MJZ 0.585106 0.914286
40 IUG 0.583333 0.810127
41 HWU 0.578947 0.901408
42 UD4 0.578947 0.914286
43 12V 0.578947 0.901408
44 F5G 0.578947 0.927536
45 F5P 0.578947 0.914286
46 CJB 0.573529 0.820895
47 UDZ 0.571429 0.853333
48 DUD 0.571429 0.913043
49 UP5 0.571429 0.853333
50 EPZ 0.56 0.914286
51 5GW 0.559524 0.942029
52 EEB 0.554455 0.901408
53 EPU 0.554455 0.901408
54 UA3 0.547945 0.939394
55 U3P 0.547945 0.939394
56 4TC 0.544554 0.831169
57 HF4 0.54321 0.942029
58 CTP 0.54321 0.942029
59 BUP 0.536585 0.928571
60 CSV 0.531915 0.851351
61 CSQ 0.531915 0.851351
62 DUT 0.52439 0.913043
63 4GW 0.516484 0.915493
64 UMA 0.513761 0.914286
65 U4S 0.513158 0.753425
66 U2P 0.506667 0.954545
67 U3S 0.5 0.753425
68 U2S 0.5 0.767123
69 FZK 0.494253 0.777778
70 PUP 0.48913 0.913043
71 U21 0.486957 0.810127
72 U20 0.486957 0.810127
73 U22 0.486957 0.790123
74 DKX 0.486486 0.746479
75 U1S 0.482759 0.75
76 0RC 0.482759 0.864865
77 2QR 0.478632 0.822785
78 5FU 0.474359 0.914286
79 LSU 0.472527 0.738095
80 8OD 0.47191 0.851351
81 C5G 0.468085 0.888889
82 7XL 0.465909 0.888889
83 UMF 0.461538 0.857143
84 G8D 0.460674 0.855263
85 2TM 0.45977 0.902778
86 UTP U U U 0.456522 0.895522
87 YSU 0.453608 0.746988
88 2TU 0.452055 0.774648
89 4RA 0.451613 0.855263
90 C2G 0.450549 0.901408
91 DU 0.45 0.898551
92 CAR 0.45 0.927536
93 UMP 0.45 0.898551
94 C5P 0.45 0.927536
95 C 0.45 0.927536
96 UAG 0.448 0.864865
97 CDC 0.446809 0.777778
98 5BU 0.444444 0.914286
99 UD0 0.444444 0.844156
100 N3E 0.440476 0.733333
101 UC5 0.440476 0.9
102 UUA 0.438356 0.772727
103 DUP 0.431818 0.887324
104 2GW 0.431373 0.901408
105 M7G 0.430108 0.780488
106 CNU 0.428571 0.927536
107 CDM 0.427083 0.842105
108 H6Y 0.425532 0.851351
109 16B 0.421687 0.888889
110 S5P 0.419753 0.915493
111 8GT 0.419355 0.855263
112 CDP MG 0.418605 0.885714
113 CXY 0.418367 0.888889
114 UPA 0.418182 0.842105
115 U2G 0.410714 0.822785
116 UML 0.408759 0.810127
117 UP6 0.407407 0.871429
118 M7M 0.40625 0.771084
119 1GW 0.40367 0.864865
120 BMP 0.402439 0.970149
121 APU 0.401786 0.828947
122 PMP UD1 0.401575 0.7875
123 DUT MG 0.4 0.857143
Similar Ligands (3D)
Ligand no: 1; 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
Ligand no: 2; Ligand: UDP; Similar ligands found: 55
No: Ligand Similarity coefficient
1 YYY 0.9739
2 TYD 0.9699
3 TBD 0.9623
4 GCQ 0.9509
5 ADP 0.9410
6 DUN 0.9317
7 D4D 0.9237
8 ADX 0.9224
9 AU1 0.9218
10 AP2 0.9215
11 SON 0.9211
12 GDP 0.9193
13 DAT 0.9189
14 IDP 0.9155
15 PRX 0.9148
16 ADP MG 0.9122
17 BEF ADP 0.9122
18 AN2 0.9115
19 A12 0.9102
20 M33 0.9098
21 CA0 0.9083
22 G5A 0.9077
23 CUU 0.9055
24 GAP 0.8984
25 DGI 0.8977
26 GNH 0.8961
27 FZQ 0.8919
28 7D3 0.8915
29 DAL AMP 0.8905
30 H2U 0.8888
31 CH 0.8874
32 AZD 0.8849
33 PSU 0.8815
34 CK7 0.8802
35 AMP 0.8793
36 FN5 0.8781
37 6AD 0.8757
38 A5A 0.8754
39 HQ5 0.8747
40 DCM 0.8724
41 8LH 0.8718
42 8GD 0.8708
43 ATY 0.8691
44 BMQ 0.8679
45 U6M 0.8672
46 NUP 0.8671
47 DC 0.8658
48 DCP 0.8657
49 TMP 0.8642
50 C8M 0.8633
51 TTP 0.8581
52 ATP 0.8570
53 DDN 0.8568
54 C2R 0.8549
55 D4T 0.8531
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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