Receptor
PDB id Resolution Class Description Source Keywords
4coj 2.48 Å EC: 1.17.4.2 CRYSTAL STRUCTURE OF THE ANAEROBIC RIBONUCLEOTIDE REDUCTASE THERMOTOGA MARITIMA IN COMPLEX WITH DATP AND CTP THERMOTOGA MARITIMA OXIDOREDUCTASE RADICAL CHEMISTRY ALLOSTERIC REGULATION ANENZYME
Ref.: THE CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA CLASS RIBONUCLEOTIDE REDUCTASE LACKS A RADICAL CYSTEINE PRE-POSITIONED IN THE ACTIVE SITE. PLOS ONE V. 10 01281 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN A:652;
B:652;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
65.409 Zn [Zn+2...
DTP B:654;
A:654;
 Valid;
Valid;
 none;
none;
 submit data
491.182 C10 H16 N5 O12 P3 c1nc(...
MG A:655;
B:655;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
24.305 Mg [Mg+2...
CTP B:653;
A:653;
 Valid;
Valid;
 none;
none;
 submit data
483.156 C9 H16 N3 O14 P3 C1=CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4COL 1.96 Å EC: 1.17.4.2 CRYSTAL STRUCTURE OF THE ANAEROBIC RIBONUCLEOTIDE REDUCTASE THERMOTOGA MARITIMA WITH DATP BOUND IN THE SPECIFICITY SITE THERMOTOGA MARITIMA OXIDOREDUCTASE RADICAL CHEMISTRY ALLOSTERIC REGULATION ANENZYME
Ref.: THE CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA CLASS RIBONUCLEOTIDE REDUCTASE LACKS A RADICAL CYSTEINE PRE-POSITIONED IN THE ACTIVE SITE. PLOS ONE V. 10 01289 2015
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4COL - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
2 4CON - CIT C6 H8 O7 C(C(=O)O)C....
3 4COJ - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4COL - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
2 4CON - CIT C6 H8 O7 C(C(=O)O)C....
3 4COJ - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4COL - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
2 4CON - CIT C6 H8 O7 C(C(=O)O)C....
3 4COJ - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
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: CTP; Similar ligands found: 95
No: Ligand ECFP6 Tc MDL keys Tc
1 HF4 1 1
2 CTP 1 1
3 CDP 0.895522 1
4 C5P 0.753623 0.985507
5 CAR 0.753623 0.985507
6 C 0.753623 0.985507
7 0RC 0.74026 0.918919
8 7XL 0.74026 0.944444
9 C2G 0.734177 0.957747
10 2TM 0.714286 0.958333
11 C5G 0.702381 0.944444
12 CDM 0.690476 0.894737
13 CDC 0.678571 0.82716
14 CXY 0.674419 0.944444
15 CDP MG 0.671053 0.942857
16 UTP 0.620253 0.942029
17 1AA 0.617021 0.906667
18 U5F 0.6125 0.942029
19 DCP 0.609756 0.90411
20 CTN 0.608696 0.857143
21 AR3 0.608696 0.857143
22 A7R 0.604167 0.931507
23 GTF 0.595238 0.90411
24 91P 0.582524 0.851852
25 I5A 0.577465 0.816901
26 DCT 0.559524 0.90411
27 UDP 0.54321 0.942029
28 CDP RB0 0.542553 0.917808
29 2AA 0.542056 0.693878
30 MCN 0.542056 0.819277
31 BUP 0.541176 0.878378
32 C3P 0.538462 0.942857
33 YYY 0.52381 0.90411
34 PMT 0.52381 0.85
35 GCQ 0.523256 0.90411
36 CSQ 0.520408 0.905405
37 CSV 0.520408 0.905405
38 16B 0.518519 0.917808
39 PCD 0.517544 0.781609
40 FZQ 0.511111 0.797619
41 C2P 0.5 0.957143
42 GPC 0.495575 0.819277
43 FN5 0.495413 0.871795
44 CSF 0.491071 0.871795
45 NCC 0.482143 0.918919
46 DKZ 0.481013 0.746667
47 HQ5 0.473684 0.758621
48 8GT 0.473118 0.907895
49 UNP 0.47191 0.915493
50 TKW 0.46988 0.971429
51 H6Y 0.463158 0.855263
52 G G 6MZ C 0.460177 0.814815
53 5HM 0.458824 0.958333
54 G C 0.45614 0.8375
55 YSC 0.455446 0.767442
56 MGT 0.453608 0.829268
57 UDH 0.452632 0.844156
58 UPP 0.452632 0.888889
59 GDU 0.447917 0.888889
60 UFM 0.447917 0.888889
61 UPG 0.447917 0.888889
62 DCM 0.447059 0.890411
63 DC 0.447059 0.890411
64 UFG 0.434343 0.842105
65 UPF 0.434343 0.842105
66 U2F 0.434343 0.842105
67 U 0.433735 0.927536
68 U5P 0.433735 0.927536
69 URM 0.43299 0.876712
70 660 0.43299 0.876712
71 UP5 0.432432 0.857143
72 5GW 0.431579 0.890411
73 0KX 0.430108 0.88
74 UPU 0.430108 0.887324
75 AWU 0.428571 0.888889
76 PRT 0.424528 0.842105
77 C5P SIA 0.423729 0.893333
78 DOC 0.423529 0.890411
79 G3N 0.421569 0.890411
80 G8D 0.421053 0.907895
81 UDX 0.42 0.888889
82 UAD 0.42 0.888889
83 2KH 0.417582 0.915493
84 3UC 0.417476 0.842105
85 4GW 0.415842 0.866667
86 UGA 0.411765 0.901408
87 UGB 0.411765 0.901408
88 USQ 0.411765 0.780488
89 V12 0.411765 0.75
90 CG2 0.410256 0.873418
91 UGF 0.407767 0.853333
92 GEO 0.407407 0.783784
93 NVG 0.403846 0.731707
94 44P 0.402299 0.902778
95 8OD 0.402062 0.855263
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: CTP; Similar ligands found: 38
No: Ligand Similarity coefficient
1 DCP MG 0.9768
2 ATP 0.9340
3 ANP 0.9332
4 BEF ADP 0.9306
5 DTP 0.9261
6 AGS 0.9211
7 GNP 0.9164
8 GTP 0.9139
9 GSP 0.9100
10 523 0.9081
11 DUT 0.9057
12 ADP ALF 0.9037
13 BEF GDP 0.9014
14 GCP 0.9014
15 ACP 0.9009
16 9GM 0.8976
17 TTP 0.8971
18 GDP BEF 0.8953
19 DBG 0.8952
20 GDP AF3 0.8952
21 ALF GDP 0.8897
22 APC 0.8893
23 GDP ALF 0.8876
24 3AT 0.8869
25 ADP BEF 0.8816
26 DUP 0.8797
27 ALF ADP 0.8743
28 GH3 0.8739
29 VO4 ADP 0.8731
30 D3T 0.8678
31 TYD 0.8658
32 DGT 0.8611
33 ADP AF3 0.8574
34 SFG 0.8566
35 D4T 0.8549
36 AD9 0.8544
37 SAM 0.8538
38 TLO 0.8527
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4COL; Ligand: DTP; 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: 4col.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4COL; Ligand: DTP; 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: 4col.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
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