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Receptor
PDB id Resolution Class Description Source Keywords
2VBU 1.7 Å EC: 2.7.1.161 RIBOFLAVIN KINASE MJ0056 FROM METHANOCALDOCOCCUS JANNASCHII IN COMPLEX WITH CDP METHANOCOCCUS JANNASCHII TRANSFERASE CRADLE-LOOP BARREL CTP-DEPENDENT KINASE FMN
Ref.: A CTP-DEPENDENT ARCHAEAL RIBOFLAVIN KINASE FORMS A BRIDGE IN THE EVOLUTION OF CRADLE-LOOP BARRELS. STRUCTURE V. 15 1577 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CDP A:1133;
Valid;
none;
submit data
403.176 C9 H15 N3 O11 P2 C1=CN...
MG A:1134;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
MRD A:1135;
A:1136;
A:1137;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
118.174 C6 H14 O2 C[C@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2VBU 1.7 Å EC: 2.7.1.161 RIBOFLAVIN KINASE MJ0056 FROM METHANOCALDOCOCCUS JANNASCHII IN COMPLEX WITH CDP METHANOCOCCUS JANNASCHII TRANSFERASE CRADLE-LOOP BARREL CTP-DEPENDENT KINASE FMN
Ref.: A CTP-DEPENDENT ARCHAEAL RIBOFLAVIN KINASE FORMS A BRIDGE IN THE EVOLUTION OF CRADLE-LOOP BARRELS. STRUCTURE V. 15 1577 2007
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2VBU - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
2 2VBV - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2VBU - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
2 2VBV - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2VBU - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
2 2VBV - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: CDP; Similar ligands found: 91
No: Ligand ECFP6 Tc MDL keys Tc
1 CDP 1 1
2 CTP 0.895522 1
3 HF4 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 C2G 0.74026 0.957747
9 CDC 0.725 0.82716
10 C5G 0.707317 0.944444
11 CDM 0.695122 0.894737
12 CXY 0.678571 0.944444
13 CTN 0.636364 0.857143
14 AR3 0.636364 0.857143
15 C C C C 0.623529 0.916667
16 1AA 0.619565 0.906667
17 C C 0.607143 0.929577
18 UDP 0.605263 0.942029
19 I5A 0.602941 0.816901
20 YYY 0.582278 0.90411
21 GCQ 0.560976 0.90411
22 C3P 0.56 0.942857
23 MCN 0.557692 0.819277
24 PMT 0.554455 0.85
25 91P 0.553398 0.851852
26 UTP 0.54321 0.942029
27 2AA 0.542857 0.693878
28 16B 0.538462 0.917808
29 CSV 0.536842 0.905405
30 CSQ 0.536842 0.905405
31 DCP 0.535714 0.90411
32 GTF 0.523256 0.90411
33 C2P 0.519481 0.957143
34 PCD 0.517857 0.781609
35 FN5 0.509434 0.871795
36 GPC 0.509091 0.819277
37 CSF 0.504587 0.871795
38 DKZ 0.5 0.746667
39 UNP 0.488372 0.915493
40 TKW 0.4875 0.971429
41 G C 0.481818 0.8375
42 5GW 0.477778 0.890411
43 5HM 0.47561 0.958333
44 A C A C 0.464912 0.835443
45 DC 0.463415 0.890411
46 DCM 0.463415 0.890411
47 U A C C 0.452174 0.846154
48 UPP 0.451613 0.888889
49 UDH 0.451613 0.844156
50 G8D 0.450549 0.907895
51 U 0.45 0.927536
52 U5P 0.45 0.927536
53 C5P SIA 0.447368 0.893333
54 URM 0.446809 0.876712
55 660 0.446809 0.876712
56 GDU 0.446809 0.888889
57 UFM 0.446809 0.888889
58 GUD 0.446809 0.888889
59 UPG 0.446809 0.888889
60 8OD 0.445652 0.855263
61 G G G C 0.444444 0.85
62 UPU 0.444444 0.887324
63 4GW 0.443299 0.866667
64 A G C C 0.440678 0.848101
65 DOC 0.439024 0.890411
66 M7G 0.43617 0.829268
67 UFG 0.43299 0.842105
68 UPF 0.43299 0.842105
69 U2F 0.43299 0.842105
70 2KH 0.431818 0.915493
71 G C C C 0.42623 0.860759
72 CG2 0.421053 0.873418
73 A U C C 0.420635 0.835443
74 G3N 0.42 0.890411
75 UDP UDP 0.418605 0.885714
76 UAD 0.418367 0.888889
77 UDX 0.418367 0.888889
78 44P 0.416667 0.902778
79 3UC 0.415842 0.842105
80 M7M 0.412371 0.797619
81 8GT 0.410526 0.907895
82 V12 0.41 0.75
83 UGB 0.41 0.901408
84 USQ 0.41 0.780488
85 UGA 0.41 0.901408
86 UP5 0.405405 0.857143
87 GEO 0.405063 0.783784
88 UDM 0.403846 0.864865
89 H6Y 0.402062 0.855263
90 NVG 0.401961 0.731707
91 CTP C C C C 0.4 0.915493
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2VBU; Ligand: CDP; Similar sites found with APoc: 180
This union binding pocket(no: 1) in the query (biounit: 2vbu.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
1 2IMG MLT None
2 5M6N 7H9 None
3 3B6C SDN None
4 3UW5 MAA CHG PRO 0DQ None
5 4XFR CIT None
6 4XG0 CIT None
7 2AK5 ARG PRO PRO LYS PRO ARG PRO ARG None
8 2BOS GLA GAL GLC NBU None
9 6FLZ MMA None
10 4P86 5GP None
11 5C2N NAG None
12 1H8P PC None
13 2DT9 THR None
14 5C9P FUC None
15 2ALG DAO None
16 3IWD M2T None
17 5YRL GLC GLC None
18 1IZC PYR 1.47059
19 5A96 GTP 2.20588
20 4U00 ADP 2.20588
21 5X80 SAL 2.20588
22 1J78 OLA 2.20588
23 5ZXD ATP 2.20588
24 1VJE MSE 2.20588
25 3LL9 ADP 2.20588
26 2RIF AMP 2.20588
27 3JQ8 DX3 2.94118
28 2GNB MAN 2.94118
29 2WD7 VGD 2.94118
30 4B5W PYR 2.94118
31 3CM2 X23 3.07692
32 3KIH GDL 3.09278
33 1Z0N BCD 3.125
34 5OQW A4E 3.14961
35 2JCB ADP 3.5
36 5C83 4YN 3.63636
37 1YXM ADE 3.67647
38 5TSH ADP 3.67647
39 3SE5 ANP 3.67647
40 5X3R 7Y3 3.67647
41 6GVZ CHO 3.67647
42 4PPF FLC 3.67647
43 2VSL MAA LYS PRO PHE 4.16667
44 1GXU 2HP 4.3956
45 1F28 UMP 4.41176
46 5GVR LMR 4.41176
47 5T63 ALA ALA ALA ALA 4.41176
48 2JBH 5GP 4.41176
49 4GLW 0XT 4.41176
50 1JI0 ATP 4.41176
51 3PUN FUC GAL NDG FUC 4.41176
52 4V1F BQ1 4.65116
53 2CBZ ATP 5.14706
54 1TLC DGP 5.14706
55 1AIQ UMP 5.14706
56 5WXU FLC 5.14706
57 1TDU DUR 5.14706
58 1SYN UMP 5.14706
59 6BR8 6OU 5.14706
60 4LSJ LSJ 5.14706
61 4ISK UMP 5.14706
62 1AXW UMP 5.14706
63 1NCE UMP 5.14706
64 2ZX2 RAM 5.14706
65 2A9W UMP 5.14706
66 2VVG ADP 5.14706
67 1DDU DDU 5.14706
68 5O74 GDP 5.14706
69 5URY PAM 5.14706
70 1JG0 UMP 5.14706
71 1ZX5 LFR 5.14706
72 6CDZ UMC 5.14706
73 1TSD UMP 5.14706
74 2R68 SUP 5.14706
75 2BHZ MAL 5.14706
76 4RW3 SHV 5.14706
77 1ZPR UMP 5.14706
78 2CHT TSA 5.51181
79 1GPM CIT 5.88235
80 1U3G ADP 5.88235
81 1TL2 NDG 5.88235
82 4FUA PGH 5.88235
83 5H4S RAM 5.88235
84 4CVN ADP 5.88235
85 1D8C GLV 5.88235
86 2CDN ADP 5.88235
87 5U32 GDP 5.88235
88 5TCI MLI 5.88235
89 1EU1 GLC 5.88235
90 6GW4 CHO 5.88235
91 3F8C HT1 6.34921
92 3KIF GDL 6.60377
93 4WGF HX2 6.61765
94 2RBK VN4 6.61765
95 4EIL UMP 6.61765
96 1RJW ETF 6.61765
97 2FJK 13P 6.61765
98 4K6B GLU 6.61765
99 3SCH TB6 6.61765
100 4ARE FLC 6.61765
101 2WOR 2AN 7
102 1NB9 ADP 7.35294
103 1NB9 RBF 7.35294
104 5W6Y TRP 7.35294
105 2PZE ATP 7.35294
106 4WZ6 ATP 7.35294
107 5Y5Q DUT 7.35294
108 1R0X ATP 7.35294
109 3A4M ADP 7.35294
110 3COB ADP 7.35294
111 2X7I CIT 7.35294
112 6HL7 CP 7.35294
113 1RRV TYD 7.35294
114 1N07 ADP 8.08823
115 3FIU POP 8.08823
116 3I6B KDO 8.08823
117 3LRE ADP 8.08823
118 2DPY ADP 8.08823
119 1N07 FMN 8.08823
120 1M2Z BOG 8.08823
121 5AZC PGT 8.08823
122 4NAE 1GP 8.08823
123 3NHB ADP 8.08823
124 2GUD MAN 8.19672
125 2GUC MAN 8.19672
126 2NUO BGC 8.19672
127 2NU5 NAG 8.19672
128 2HYR BGC GLC 8.19672
129 1JJ7 ADP 8.82353
130 1G6H ADP 8.82353
131 5YJS SAL 8.82353
132 6A20 ADP 8.82353
133 5CX8 TG6 8.82353
134 3C1M ANP 8.82353
135 5XXS COA 9.09091
136 2AWN ADP 9.55882
137 2W58 ADP 9.55882
138 1RRC ADP 9.55882
139 1L7N ALF 9.55882
140 1YQT ADP 9.55882
141 5YV5 ADP 10.2941
142 1OYJ GSH 10.2941
143 5H2U 1N1 11.0294
144 5FUI APY 11.3636
145 2QQD AG2 11.6071
146 2PNC CLU 11.7647
147 5L2R MLA 12.5
148 1DCP HBI 12.5
149 3KC1 2T6 12.5
150 2FB3 5AD 12.5
151 5DNK SAH 13.2353
152 3KPE TM3 13.7255
153 3QDV NDG 13.9706
154 3QDW NDG 13.9706
155 3QDY CBS 13.9706
156 3QDX CBS 13.9706
157 1UCD U5P 14.7059
158 1MT1 AG2 15.3846
159 2OBM ADP 15.4412
160 1GOJ ADP 15.4412
161 2D2F ADP 15.4412
162 1B0U ATP 15.4412
163 5LWY OLB 16.8224
164 1T5C ADP 16.9118
165 2AKO ADP 16.9118
166 5A89 ADP 17.6471
167 5A89 FMN 17.6471
168 1R6N 434 17.6471
169 1EXF GLY 17.6471
170 4P83 U5P 17.6471
171 2QES ADE 17.6471
172 3H4S ADP 18.3824
173 4FRZ ADP 18.3824
174 2AAZ UMP 19.1176
175 2IU8 PLM 19.1176
176 2XN5 FUN 19.8529
177 4AG5 ADP 19.8529
178 5W7B MYR 21.3235
179 3ZIA ADP 22.2222
180 5NXX 3Q7 39.7059
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