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Receptor
PDB id Resolution Class Description Source Keywords
3CI3 1.11 Å EC: 2.5.1.17 STRUCTURE OF THE PDUO-TYPE ATP:CO(I)RRINOID ADENOSYLTRANSFER LACTOBACILLUS REUTERI COMPLEXED WITH PARTIAL ADENOSYLCOBALAP PPI LACTOBACILLUS REUTERI ADENOSYLTRANSFERASE VARIANT ADENOSYLCOBALAMIN BINDING ATP TRANSFERASE
Ref.: STRUCTURAL CHARACTERIZATION OF A HUMAN-TYPE CORRINO ADENOSYLTRANSFERASE CONFIRMS THAT COENZYME B12 IS SYNTHESIZED THROUGH A FOUR-COORDINATE INTERMEDIATE. BIOCHEMISTRY V. 47 5755 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3PO A:901;
Valid;
none;
submit data
257.955 H5 O10 P3 OP(=O...
5AD A:902;
Valid;
none;
submit data
251.242 C10 H13 N5 O3 C[C@@...
B12 A:800;
Part of Protein;
none;
submit data
1330.36 C62 H89 Co N13 O14 P Cc1cc...
MG A:190;
Invalid;
none;
submit data
24.305 Mg [Mg+2...
NA A:189;
Part of Protein;
none;
submit data
22.99 Na [Na+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3CI3 1.11 Å EC: 2.5.1.17 STRUCTURE OF THE PDUO-TYPE ATP:CO(I)RRINOID ADENOSYLTRANSFER LACTOBACILLUS REUTERI COMPLEXED WITH PARTIAL ADENOSYLCOBALAP PPI LACTOBACILLUS REUTERI ADENOSYLTRANSFERASE VARIANT ADENOSYLCOBALAMIN BINDING ATP TRANSFERASE
Ref.: STRUCTURAL CHARACTERIZATION OF A HUMAN-TYPE CORRINO ADENOSYLTRANSFERASE CONFIRMS THAT COENZYME B12 IS SYNTHESIZED THROUGH A FOUR-COORDINATE INTERMEDIATE. BIOCHEMISTRY V. 47 5755 2008
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3CI1 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
2 3CI3 - 5AD C10 H13 N5 O3 C[C@@H]1[C....
3 3GAH - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 3CI4 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
5 3GAI - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
6 3GAJ - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3CI1 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
2 3CI3 - 5AD C10 H13 N5 O3 C[C@@H]1[C....
3 3GAH - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 3CI4 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
5 3GAI - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
6 3GAJ - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
7 2NT8 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3CI1 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
2 3CI3 - 5AD C10 H13 N5 O3 C[C@@H]1[C....
3 3GAH - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 3CI4 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
5 3GAI - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
6 3GAJ - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
7 6D5X - 5AD C10 H13 N5 O3 C[C@@H]1[C....
8 2IDX - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
9 2NT8 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 3PO; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 3PO 1 1
2 6YW 0.764706 1
3 PPV 0.6 1
4 PIS 0.5 0.84
5 P22 0.44 0.75
Ligand no: 2; Ligand: 5AD; Similar ligands found: 203
No: Ligand ECFP6 Tc MDL keys Tc
1 5AD 1 1
2 ADN 0.672727 0.854839
3 RAB 0.672727 0.854839
4 XYA 0.672727 0.854839
5 5N5 0.649123 0.854839
6 Y3J 0.649123 0.929825
7 MTA 0.639344 0.857143
8 5CD 0.637931 0.868852
9 A4D 0.637931 0.854839
10 EP4 0.633333 0.830769
11 M2T 0.622951 0.80597
12 DTA 0.596774 0.815385
13 3DH 0.59375 0.857143
14 CC5 0.568965 0.883333
15 7D7 0.568965 0.793651
16 S4M 0.565217 0.72
17 AOC 0.558824 0.828125
18 NEC 0.558824 0.885246
19 ZAS 0.552239 0.791045
20 A 0.552239 0.768116
21 AMP 0.552239 0.768116
22 LMS 0.552239 0.670886
23 ABM 0.550725 0.771429
24 A3N 0.550725 0.815385
25 6RE 0.544118 0.757143
26 SRA 0.544118 0.726027
27 3AM 0.537313 0.753623
28 DSH 0.536232 0.768116
29 MAO 0.535211 0.710526
30 3AD 0.532258 0.83871
31 SP1 0.529412 0.722222
32 RP1 0.529412 0.722222
33 J7C 0.528571 0.768116
34 A2D 0.528571 0.746479
35 5AS 0.527778 0.650602
36 GJV 0.521127 0.746479
37 SON 0.520548 0.716216
38 A3G 0.514286 0.80303
39 A12 0.513889 0.716216
40 BA3 0.513889 0.746479
41 AP2 0.513889 0.716216
42 M33 0.513514 0.760563
43 AU1 0.513514 0.726027
44 MHZ 0.513514 0.710526
45 AP5 0.506849 0.746479
46 B4P 0.506849 0.746479
47 ADP 0.506849 0.746479
48 AN2 0.5 0.736111
49 A7D 0.5 0.80303
50 2AM 0.5 0.742857
51 SAM 0.5 0.75
52 PRX 0.5 0.75
53 AT4 0.5 0.716216
54 SA8 0.493506 0.771429
55 AD9 0.493506 0.726027
56 ADX 0.493333 0.670886
57 CA0 0.493333 0.726027
58 2BA 0.493151 0.764706
59 A3P 0.493151 0.742857
60 CMP 0.493151 0.776119
61 HEJ 0.486842 0.746479
62 50T 0.486842 0.736111
63 5X8 0.486842 0.815385
64 ACP 0.486842 0.726027
65 A3T 0.486842 0.857143
66 ATP 0.486842 0.746479
67 SFG 0.486842 0.828125
68 7D5 0.485294 0.684932
69 9ZA 0.481928 0.72
70 9ZD 0.481928 0.72
71 SMM 0.481481 0.72
72 ANP 0.481013 0.726027
73 5FA 0.480519 0.746479
74 APR 0.480519 0.746479
75 AR6 0.480519 0.746479
76 APC 0.480519 0.716216
77 AQP 0.480519 0.746479
78 A3S 0.48 0.815385
79 OVE 0.478873 0.712329
80 AAT 0.475 0.746479
81 5AL 0.475 0.760563
82 EEM 0.475 0.75
83 A5D 0.474359 0.815385
84 ADV 0.474359 0.716216
85 SAP 0.474359 0.706667
86 AGS 0.474359 0.706667
87 ADP PO3 0.474359 0.768116
88 RBY 0.474359 0.716216
89 QQX 0.471429 0.708333
90 5F1 0.469697 0.78125
91 A5A 0.469136 0.675
92 SAI 0.468354 0.779412
93 G5A 0.468354 0.630952
94 SAH 0.468354 0.791045
95 103 0.464789 0.764706
96 QQY 0.464789 0.71831
97 ACK 0.464789 0.761194
98 S7M 0.463415 0.75
99 ACQ 0.4625 0.726027
100 T99 0.4625 0.716216
101 GAP 0.4625 0.726027
102 TAT 0.4625 0.716216
103 3L1 0.461538 0.772727
104 3D1 0.461538 0.772727
105 54H 0.457831 0.658537
106 52H 0.457831 0.650602
107 VMS 0.457831 0.658537
108 PAP 0.455696 0.732394
109 A2P 0.453333 0.753623
110 NOC 0.453125 0.790323
111 5I5 0.453125 0.913793
112 53H 0.452381 0.650602
113 DAL AMP 0.452381 0.760563
114 MAP 0.452381 0.706667
115 TSB 0.452381 0.666667
116 ADP ALF 0.451219 0.706667
117 ATF 0.451219 0.716216
118 ALF ADP 0.451219 0.706667
119 2VA 0.448718 0.830769
120 8QN 0.447059 0.760563
121 5SV 0.447059 0.710526
122 6YZ 0.445783 0.726027
123 SRP 0.445783 0.716216
124 VO4 ADP 0.445783 0.736111
125 SSA 0.445783 0.630952
126 ADP VO4 0.445783 0.736111
127 LSS 0.44186 0.635294
128 0UM 0.44186 0.760563
129 PAJ 0.44186 0.701299
130 7D3 0.44 0.666667
131 PPS 0.439024 0.65
132 1ZZ 0.438202 0.683544
133 NVA 2AD 0.4375 0.782609
134 62X 0.436782 0.72
135 NVA LMS 0.436782 0.627907
136 A22 0.435294 0.736111
137 D3Y 0.435294 0.791045
138 8X1 0.435294 0.609195
139 5CA 0.435294 0.630952
140 KB1 0.433333 0.736111
141 MYR AMP 0.433333 0.683544
142 ARJ 0.432836 0.774194
143 VRT 0.432099 0.794118
144 SO8 0.432099 0.818182
145 9X8 0.431818 0.72973
146 LEU LMS 0.431818 0.627907
147 K15 0.431818 0.739726
148 OAD 0.431818 0.75
149 S8M 0.430233 0.757143
150 OOB 0.430233 0.736111
151 GEK 0.430233 0.757143
152 25A 0.430233 0.746479
153 WAQ 0.426966 0.697368
154 GSU 0.426966 0.630952
155 3NZ 0.426966 0.782609
156 ADZ 0.425926 0.618182
157 AMO 0.425287 0.716216
158 ADQ 0.425287 0.726027
159 A1R 0.425287 0.697368
160 NSS 0.425287 0.630952
161 DSZ 0.425287 0.630952
162 A3R 0.425287 0.697368
163 4AD 0.425287 0.706667
164 2A5 0.425 0.68
165 TXA 0.422222 0.739726
166 BIS 0.422222 0.697368
167 9K8 0.422222 0.627907
168 3OD 0.422222 0.75
169 ME8 0.422222 0.683544
170 PTJ 0.422222 0.710526
171 SXZ 0.422222 0.75
172 00A 0.420455 0.697368
173 DLL 0.420455 0.736111
174 AHX 0.420455 0.688312
175 ATR 0.419753 0.742857
176 7D4 0.417722 0.666667
177 TAD 0.416667 0.679487
178 ADP BMA 0.41573 0.726027
179 3UK 0.41573 0.726027
180 A6D 0.41573 0.716216
181 26A 0.411765 0.787879
182 AFX 0.411765 0.716418
183 LAD 0.411111 0.679487
184 KAA 0.411111 0.609195
185 PR8 0.411111 0.670886
186 B5V 0.411111 0.716216
187 P5A 0.411111 0.602273
188 A A 0.411111 0.746479
189 V3L 0.409639 0.746479
190 B5M 0.408602 0.72973
191 YAP 0.408602 0.706667
192 B5Y 0.408602 0.72973
193 0XU 0.407407 0.828125
194 FYA 0.406593 0.736111
195 JB6 0.406593 0.697368
196 NB8 0.406593 0.688312
197 YSA 0.404255 0.630952
198 ZDA 0.402439 0.742857
199 25L 0.402174 0.736111
200 A A A 0.4 0.736111
201 101 0.4 0.708333
202 4UV 0.4 0.706667
203 TYR AMP 0.4 0.706667
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3CI3; Ligand: 3PO; Similar sites found with APoc: 7
This union binding pocket(no: 1) in the query (biounit: 3ci3.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 4PPF FLC 3.60825
2 1FQK ALF 4.12371
3 1FQJ ALF 4.12371
4 1KSK URA 4.63918
5 2Q8M AMP 7.73196
6 1B8U OAA 10.3093
7 6EOM ALA LYS 26.8041
Pocket No.: 2; Query (leader) PDB : 3CI3; Ligand: 3PO; 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: 3ci3.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3CI3; Ligand: 3PO; 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: 3ci3.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3CI3; Ligand: 5AD; Similar sites found with APoc: 7
This union binding pocket(no: 4) in the query (biounit: 3ci3.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 4PPF FLC 3.60825
2 1FQK ALF 4.12371
3 1FQJ ALF 4.12371
4 1KSK URA 4.63918
5 2Q8M AMP 7.73196
6 1B8U OAA 10.3093
7 6EOM ALA LYS 26.8041
Pocket No.: 5; Query (leader) PDB : 3CI3; Ligand: 5AD; 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: 3ci3.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 3CI3; Ligand: 5AD; 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: 3ci3.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
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