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Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DTP B:702;
A:702;
Valid;
Valid;
none;
none;
submit data
491.182 C10 H16 N5 O12 P3 c1nc(...
SFO B:1633;
A:1631;
Invalid;
Invalid;
none;
none;
submit data
83.087 H3 O3 S O[SH]...
ZN A:700;
B:700;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
MG A:701;
B:701;
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
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
Ligand no: 1; Ligand: DTP; Similar ligands found: 167
No: Ligand ECFP6 Tc MDL keys Tc
1 DTP 1 1
2 DAT 0.891892 1
3 D5M 0.773333 0.971831
4 DA 0.773333 0.971831
5 AS 0.696203 0.92
6 DDS 0.694118 0.944444
7 HF7 0.689655 0.986111
8 3AT 0.655172 0.931507
9 7D4 0.635294 0.893333
10 ATP 0.627907 0.905405
11 HEJ 0.627907 0.905405
12 3D1 0.626667 0.835616
13 3L1 0.626667 0.835616
14 5FA 0.62069 0.905405
15 AQP 0.62069 0.905405
16 CPA 0.584906 0.8625
17 ZDA 0.577778 0.853333
18 B4P 0.574713 0.88
19 AP5 0.574713 0.88
20 5F1 0.56962 0.794521
21 BA3 0.563218 0.88
22 DGT 0.557895 0.909091
23 ADP 0.556818 0.905405
24 101 0.552941 0.917808
25 7D3 0.551724 0.893333
26 A2D 0.54023 0.88
27 DOI 0.539326 0.917808
28 2A5 0.532609 0.932432
29 6YZ 0.53125 0.906667
30 25L 0.529412 0.893333
31 SAP 0.526882 0.858974
32 PAP 0.526882 0.917808
33 AGS 0.526882 0.858974
34 ATR 0.526882 0.930556
35 TAT 0.515789 0.87013
36 T99 0.515789 0.87013
37 103 0.505747 0.826667
38 AN2 0.5 0.893333
39 AR6 0.5 0.88
40 AT4 0.5 0.87013
41 ACQ 0.5 0.906667
42 APR 0.5 0.88
43 A1R 0.49505 0.921053
44 A3R 0.49505 0.921053
45 AD9 0.494737 0.881579
46 M33 0.494624 0.868421
47 AV2 0.489796 0.88
48 ACP 0.489362 0.906667
49 A 0.488636 0.878378
50 AMP 0.488636 0.878378
51 7D5 0.488372 0.866667
52 T5A 0.486957 0.853659
53 NA7 0.485437 0.945946
54 DGI 0.484536 0.909091
55 ANP 0.484536 0.881579
56 128 0.482143 0.747126
57 A2R 0.48 0.893333
58 ADX 0.478723 0.795181
59 CA0 0.478723 0.857143
60 A22 0.475248 0.893333
61 HDV 0.474747 0.881579
62 HFD 0.474227 0.858974
63 ABM 0.472527 0.831169
64 APC 0.46875 0.92
65 PRX 0.46875 0.833333
66 ADQ 0.466019 0.857143
67 PPS 0.464646 0.817073
68 ITT 0.463158 0.853333
69 6OG 0.463158 0.907895
70 A2P 0.462366 0.916667
71 A3P 0.462366 0.90411
72 DA DT DA DA 0.460317 0.829268
73 ATF 0.46 0.87013
74 50T 0.458333 0.868421
75 N5P 0.456311 0.797468
76 4AD 0.451923 0.883117
77 5AL 0.45 0.844156
78 3OD 0.448598 0.857143
79 A12 0.446809 0.92
80 AP2 0.446809 0.92
81 G5P 0.446429 0.8375
82 A4P 0.444444 0.790698
83 UP5 0.443478 0.835443
84 9X8 0.443396 0.835443
85 OAD 0.443396 0.857143
86 MDR 0.44186 0.783784
87 SRP 0.441176 0.87013
88 7DT 0.438776 0.891892
89 G3A 0.4375 0.8375
90 AP0 0.435897 0.814815
91 NB8 0.435185 0.860759
92 SRA 0.434783 0.833333
93 00A 0.433962 0.802469
94 DLL 0.433962 0.844156
95 2AM 0.433333 0.90411
96 AU1 0.43299 0.881579
97 DCP 0.43299 0.831169
98 6V0 0.431034 0.814815
99 NAI 0.431034 0.825
100 GTA 0.429825 0.807229
101 8QN 0.428571 0.844156
102 25A 0.428571 0.88
103 3AM 0.428571 0.864865
104 5SV 0.428571 0.814815
105 OOB 0.428571 0.844156
106 9SN 0.427273 0.792683
107 PR8 0.425926 0.8625
108 WAQ 0.425926 0.871795
109 V3L 0.425743 0.88
110 NDP 0.425 0.8375
111 139 0.425 0.8625
112 AMO 0.424528 0.894737
113 PAJ 0.424528 0.804878
114 FYA 0.422018 0.893333
115 PTJ 0.422018 0.814815
116 1ZZ 0.422018 0.807229
117 BIS 0.422018 0.848101
118 NZQ 0.421488 0.85
119 ADV 0.42 0.894737
120 ADP PO3 0.42 0.853333
121 RBY 0.42 0.894737
122 OVE 0.419355 0.868421
123 MAP 0.419048 0.858974
124 GGZ 0.419048 0.792683
125 TXD 0.418803 0.848101
126 3AD 0.418605 0.77027
127 ALF ADP 0.417476 0.790123
128 ADP ALF 0.417476 0.790123
129 3UK 0.416667 0.833333
130 TXE 0.415254 0.848101
131 0WD 0.414634 0.8375
132 12D 0.413793 0.755814
133 LAD 0.412844 0.85
134 B5V 0.412844 0.822785
135 GAP 0.411765 0.810127
136 2FD 0.411111 0.805195
137 FA5 0.410714 0.87013
138 YAP 0.410714 0.858974
139 48N 0.410256 0.8375
140 CNA 0.409836 0.87013
141 TXP 0.409836 0.860759
142 PUA 0.409449 0.897436
143 ME8 0.409091 0.807229
144 TXA 0.409091 0.846154
145 AFH 0.408696 0.82716
146 SON 0.408163 0.894737
147 DGP 0.408163 0.896104
148 DG 0.408163 0.896104
149 AHX 0.407407 0.860759
150 DND 0.40678 0.846154
151 NXX 0.40678 0.846154
152 NAX 0.40678 0.839506
153 NJP 0.406504 0.858974
154 DAL AMP 0.40566 0.820513
155 DQV 0.405172 0.868421
156 7D7 0.404762 0.733333
157 OMR 0.403361 0.819277
158 GH3 0.401869 0.858974
159 LAQ 0.401709 0.807229
160 NPW 0.401639 0.851852
161 ADS THS THS THS 0.401575 0.770115
162 XYA 0.4 0.76
163 ADP VO4 0.4 0.844156
164 VO4 ADP 0.4 0.844156
165 CL9 0.4 0.805195
166 RAB 0.4 0.76
167 ADN 0.4 0.76
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: 203
This union binding pocket(no: 1) in the query (biounit: 4col.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 5MWE TCE None
2 4WG0 CHD None
3 4V1F BQ1 None
4 2ZWS PLM 0.928793
5 5IM3 DTP 1.07527
6 3E7O 35F 1.38889
7 2RH1 CAU 1.4
8 4UNR QZE 1.42857
9 5CX8 TG6 1.4553
10 1EU1 GLC 1.5361
11 1CZA ADP 1.5361
12 3COW 52H 1.66113
13 1U3D FAD 1.76817
14 5B4B LP5 2.01613
15 1ZED PNP 2.06612
16 5A8E XTK 2.15054
17 4ZW3 4S9 2.15054
18 5FPN KYD 2.1875
19 1PZO CBT 2.28137
20 2Z7I 742 2.35294
21 5ZKC 3C0 2.3753
22 2J1P GRG 2.38908
23 2YIV YIV 2.45776
24 3HP9 CF1 2.48963
25 5EQ8 HSO 2.52708
26 3E3U NVC 2.53807
27 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 2.6087
28 2Q8G AZX 2.7027
29 3UR0 SVR 2.71845
30 5CX6 CDP 2.76498
31 2PX6 DH9 2.8481
32 3KDU NKS 2.88809
33 4QEK GLC 2.91859
34 2BIF BOG 2.98507
35 4XJ7 ADN 2.99625
36 5NM7 GLY 3.00752
37 1M48 FRG 3.00752
38 3GKJ HC3 3.01724
39 4RJD TFP 3.0303
40 4J6O CIT 3.0303
41 1J78 OLA 3.05677
42 4KBS PX2 3.25581
43 4YC9 4C1 3.26087
44 2XXP DSL 3.26633
45 6MVU K4V 3.37942
46 5BU2 ADP 3.52423
47 4HEE 14R 3.5461
48 5JH2 A2P 3.54839
49 2HHP FLC 3.58491
50 2P4Y C03 3.61011
51 5KAX RHQ 3.61446
52 4URF 1PS 3.62903
53 5DCH 1YO 3.64583
54 3E70 GDP 3.65854
55 3AQT RCO 3.67347
56 3FUR Z12 3.67647
57 1R6N 434 3.68664
58 3NB0 G6P 3.68664
59 1MI3 NAD 3.72671
60 4LY9 S6P 3.76766
61 4LY9 1YY 3.76766
62 1GPM CIT 3.80952
63 5HCN DAO 3.83142
64 2GBB CIT 3.84615
65 6MPT C30 3.84615
66 3MAG 3MA 3.90879
67 4OB6 S2T 4.10557
68 6ESN BWE 4.11985
69 4DR9 BB2 4.16667
70 3TUR DGL 4.18118
71 1M5B BN1 4.18251
72 2VBQ BSJ 4.24242
73 5WIU AQD 4.50237
74 3FXU TSU 4.59016
75 3SQP 3J8 4.60251
76 5NTP 98E 4.62185
77 6BR9 PGV 4.73538
78 6C7R EO4 4.8
79 5B0W 22B 4.811
80 2CDC XYS 4.91803
81 1DTL BEP 4.96894
82 2FV5 541 4.98084
83 3G58 988 4.98688
84 2G36 TRP 5
85 4UBS DIF 5.08906
86 2AJH MET 5.10204
87 5FUS DAO 5.22648
88 1XMY ROL 5.27638
89 5LX9 OLB 5.28169
90 3KP6 SAL 5.29801
91 1NQ7 HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU 5.32787
92 5LOF 70R 5.40541
93 5KAU RHQ 5.45455
94 5OSW DIU 5.48885
95 3SFI 3SF 5.50847
96 5FH7 5XL 5.64516
97 5IF4 6AK 5.66038
98 3D04 SAK 5.66038
99 2QCX PF1 5.70342
100 5KD8 TNR 5.72451
101 1TO9 HMH 5.76923
102 4U0S ADP 5.81395
103 1RL4 BL5 5.85106
104 4DXG NDG FUC SIA GAL 5.88235
105 2A1L PCW 5.92593
106 1NP7 FAD 5.93047
107 5AAV GW5 5.95238
108 5U75 SIA GAL NDG FUC 5.95238
109 3CHT 4NB 5.95238
110 5AZC PGT 6
111 2WOR 2AN 6
112 3TTZ 07N 6.06061
113 3IWK NAD 6.16302
114 3O01 DXC 6.16883
115 5CSD ACD 6.28931
116 5IUC SIA GAL A2G 6.29921
117 5G3N X28 6.29921
118 2D5Z L35 6.38298
119 4P8O 883 6.41711
120 2ZCQ B65 6.48464
121 3EE4 MYR 6.50155
122 1LQY BB2 6.52174
123 5L7G LYS SER LEU LEU GLN GLN LEU LEU THR GLU 6.55738
124 5CHR 4NC 6.56934
125 5MTE BB2 6.56934
126 2BMB PMM 6.6055
127 4AUT FAD 6.83761
128 3B9Z CO2 6.95876
129 4KJU 1RH 6.97674
130 3KYQ DPV 7.03518
131 1DEK DGP 7.05394
132 1XX4 BAM 7.27969
133 2FKW RG1 7.31707
134 5V3Y 5V8 7.34266
135 3H0A D30 7.45614
136 2BCG GER 7.50552
137 4WGF HX2 7.80488
138 4F7E 0SH 8.16327
139 5C9J DAO 8.18505
140 5Y02 HBX 8.41121
141 5UGW GSH 8.57143
142 4XIZ LPP 8.57143
143 5Z6T NAP 8.74636
144 3WUR O4B 8.77193
145 2UW1 GVM 8.87574
146 1ZPD CIT 8.97887
147 4F4S EFO 9.21053
148 5W7B MYR 9.21986
149 4OGQ 7PH 9.30931
150 4OGQ 1O2 9.30931
151 3N7S 3N7 9.375
152 5U98 1KX 9.38628
153 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 9.52381
154 3RMK BML 9.63855
155 4ZGM 32M 9.67742
156 4UCC ZKW 9.87124
157 5OLK DTP 10
158 3E8T UQ8 10
159 1G27 BB1 10.119
160 3NJQ NJQ 10.3627
161 3WCA FPS 10.411
162 1T0S BML 10.4651
163 5V4R MGT 10.4938
164 1RV1 IMZ 10.5882
165 5XS3 VAL ARG SER ARG ARG CYS LEU ARG LEU 11.2245
166 4D1J DGJ 11.6667
167 5J6H NCA 12
168 2Z8L NAG FUC SIA GAL 12.0192
169 3G08 FEE 12.1212
170 5N7O 69Y 12.2172
171 3L1N PLM 12.3711
172 5OCA 9QZ 12.605
173 1ZEI CRS 13.2075
174 3KXC PLM 13.4021
175 1NF8 BOG 13.5266
176 4B7P 9UN 14.3478
177 2ZFZ ARG 15.1899
178 6BR8 PGV 15.873
179 5XJD 87L 15.9091
180 5C1M CLR 16
181 3R9V DXC 16.0839
182 5NNT DPV 16.2162
183 2VWA PTY 16.8317
184 5M37 9SZ 17.3913
185 5M36 9SZ 17.4672
186 5LJ0 6XX 17.6923
187 4CS9 AMP 18.5185
188 4JE7 BB2 20.8122
189 3TL1 JRO 21.3836
190 3T6E UQ9 24.031
191 5ZCO CHD 24.7059
192 2DYS TGL 24.7059
193 5W97 CHD 24.7059
194 5ZCO PGV 24.7059
195 2DYR TGL 24.7059
196 5Z84 TGL 24.7059
197 5Z84 PGV 24.7059
198 2DYR PGV 24.7059
199 2DYS PGV 24.7059
200 5ZCO TGL 24.7059
201 5ZCO PEK 24.7059
202 5Z84 CHD 24.7059
203 2Y69 CHD 31.746
204 4JMU 1ML 50
Pocket No.: 2; Query (leader) PDB : 4COL; Ligand: DTP; Similar sites found with APoc: 35
This union binding pocket(no: 2) in the query (biounit: 4col.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 3GDN HBX 1.72745
2 4YDQ HFG 1.81087
3 3WYJ H78 1.97628
4 6DIO CIT 2.0979
5 3PE2 E1B 2.67062
6 1TMX HGX 2.73038
7 4IBF 1D5 3.10078
8 3W54 RNB 3.34347
9 1XQP 8HG 3.51562
10 2HFP NSI 3.5461
11 3RWP ABQ 3.85852
12 4DDY DN6 4.18251
13 1Q7E MET 4.20561
14 2F7A BEZ 4.31034
15 5XKT GNP 4.5
16 3G5K BB2 4.91803
17 1QMG DMV 5.53435
18 5OGX FAD 5.95238
19 4KVL PLM 5.99078
20 5C79 PBU 6
21 6B2W AG2 7.20721
22 4XUB 43D 7.69231
23 1HBK MYR 7.86517
24 2P4Q FLC 8.04829
25 1SBR VIB 9.5
26 2WBV SIA 9.52381
27 4GN8 ASO 10.0334
28 4YEF 4CQ 10.1124
29 1L0I PSR 10.2564
30 4K90 MLA 10.6977
31 3QUZ QUV 12.1212
32 4URX FK1 15.6757
33 4FLP JQ1 18.4874
34 5N18 8HZ 22.0183
35 3KMZ EQO 26.3158
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