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: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 3PO 1 1
2 9PI 0.764706 1
3 6YW 0.764706 1
4 PPV 0.6 1
5 PIS 0.5 0.84
6 P22 0.44 0.75
Ligand no: 2; Ligand: 5AD; Similar ligands found: 217
No: Ligand ECFP6 Tc MDL keys Tc
1 5AD 1 1
2 XYA 0.672727 0.854839
3 ADN 0.672727 0.854839
4 RAB 0.672727 0.854839
5 Y3J 0.649123 0.929825
6 5N5 0.649123 0.854839
7 MTA 0.639344 0.857143
8 A4D 0.637931 0.854839
9 5CD 0.637931 0.868852
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 7D7 0.568965 0.793651
15 CC5 0.568965 0.883333
16 S4M 0.565217 0.72
17 NEC 0.558824 0.885246
18 AOC 0.558824 0.828125
19 LMS 0.552239 0.670886
20 ZAS 0.552239 0.791045
21 AMP 0.552239 0.768116
22 A 0.552239 0.768116
23 A3N 0.550725 0.815385
24 45A 0.550725 0.771429
25 ABM 0.550725 0.771429
26 SRA 0.544118 0.726027
27 6RE 0.544118 0.757143
28 3AM 0.537313 0.753623
29 N5O 0.536232 0.815385
30 DSH 0.536232 0.768116
31 MAO 0.535211 0.710526
32 3AD 0.532258 0.83871
33 RP1 0.529412 0.722222
34 SP1 0.529412 0.722222
35 J7C 0.528571 0.768116
36 A2D 0.528571 0.746479
37 5AS 0.527778 0.650602
38 GJV 0.521127 0.746479
39 N5A 0.521127 0.84127
40 SON 0.520548 0.716216
41 A3G 0.514286 0.80303
42 A12 0.513889 0.716216
43 BA3 0.513889 0.746479
44 AP2 0.513889 0.716216
45 M33 0.513514 0.760563
46 AU1 0.513514 0.726027
47 MHZ 0.513514 0.710526
48 B4P 0.506849 0.746479
49 ADP 0.506849 0.746479
50 AP5 0.506849 0.746479
51 H1Q 0.506667 0.757143
52 2AM 0.5 0.742857
53 A7D 0.5 0.80303
54 PRX 0.5 0.75
55 AN2 0.5 0.736111
56 ADP MG 0.5 0.768116
57 AT4 0.5 0.716216
58 SAM 0.5 0.75
59 AD9 0.493506 0.726027
60 SA8 0.493506 0.771429
61 ADX 0.493333 0.670886
62 CA0 0.493333 0.726027
63 2BA 0.493151 0.764706
64 A3P 0.493151 0.742857
65 CMP 0.493151 0.776119
66 HEJ 0.486842 0.746479
67 SFG 0.486842 0.828125
68 KG4 0.486842 0.726027
69 5X8 0.486842 0.815385
70 50T 0.486842 0.736111
71 A3T 0.486842 0.857143
72 ATP 0.486842 0.746479
73 ACP 0.486842 0.726027
74 7D5 0.485294 0.684932
75 9ZD 0.481928 0.72
76 9ZA 0.481928 0.72
77 SMM 0.481481 0.72
78 8LH 0.481481 0.739726
79 ANP 0.481013 0.726027
80 AQP 0.480519 0.746479
81 5FA 0.480519 0.746479
82 AR6 0.480519 0.746479
83 APC 0.480519 0.716216
84 APR 0.480519 0.746479
85 A3S 0.48 0.815385
86 OVE 0.478873 0.712329
87 5AL 0.475 0.760563
88 EEM 0.475 0.75
89 AAT 0.475 0.746479
90 8LE 0.475 0.72973
91 SAP 0.474359 0.706667
92 A5D 0.474359 0.815385
93 ADV 0.474359 0.716216
94 RBY 0.474359 0.716216
95 APC MG 0.474359 0.746479
96 ADP PO3 0.474359 0.768116
97 ATP MG 0.474359 0.768116
98 AGS 0.474359 0.706667
99 QQX 0.471429 0.708333
100 5F1 0.469697 0.78125
101 A5A 0.469136 0.675
102 G5A 0.468354 0.630952
103 SAI 0.468354 0.779412
104 SAH 0.468354 0.791045
105 QQY 0.464789 0.71831
106 ACK 0.464789 0.761194
107 103 0.464789 0.764706
108 S7M 0.463415 0.75
109 TAT 0.4625 0.716216
110 T99 0.4625 0.716216
111 GAP 0.4625 0.726027
112 ACQ 0.4625 0.726027
113 3L1 0.461538 0.772727
114 3D1 0.461538 0.772727
115 52H 0.457831 0.650602
116 54H 0.457831 0.658537
117 VMS 0.457831 0.658537
118 PAP 0.455696 0.732394
119 A2P 0.453333 0.753623
120 5I5 0.453125 0.913793
121 NOC 0.453125 0.790323
122 8LQ 0.452381 0.739726
123 MAP 0.452381 0.706667
124 TSB 0.452381 0.666667
125 DAL AMP 0.452381 0.760563
126 53H 0.452381 0.650602
127 ALF ADP 0.451219 0.706667
128 ADP ALF 0.451219 0.706667
129 ATF 0.451219 0.716216
130 2VA 0.448718 0.830769
131 8QN 0.447059 0.760563
132 5SV 0.447059 0.710526
133 VO4 ADP 0.445783 0.736111
134 ADP VO4 0.445783 0.736111
135 SRP 0.445783 0.716216
136 SSA 0.445783 0.630952
137 6YZ 0.445783 0.726027
138 PAJ 0.44186 0.701299
139 0UM 0.44186 0.760563
140 LSS 0.44186 0.635294
141 HQG 0.440476 0.736111
142 7D3 0.44 0.666667
143 PPS 0.439024 0.65
144 1ZZ 0.438202 0.683544
145 NVA 2AD 0.4375 0.782609
146 62X 0.436782 0.72
147 NVA LMS 0.436782 0.627907
148 D3Y 0.435294 0.791045
149 5CA 0.435294 0.630952
150 A22 0.435294 0.736111
151 8X1 0.435294 0.609195
152 MYR AMP 0.433333 0.683544
153 KB1 0.433333 0.736111
154 ARJ 0.432836 0.774194
155 VRT 0.432099 0.794118
156 SO8 0.432099 0.818182
157 9X8 0.431818 0.72973
158 K15 0.431818 0.739726
159 OAD 0.431818 0.75
160 LEU LMS 0.431818 0.627907
161 OZV 0.430233 0.746479
162 25A 0.430233 0.746479
163 OOB 0.430233 0.736111
164 GEK 0.430233 0.757143
165 S8M 0.430233 0.757143
166 3NZ 0.426966 0.782609
167 WAQ 0.426966 0.697368
168 GSU 0.426966 0.630952
169 ADZ 0.425926 0.618182
170 DSZ 0.425287 0.630952
171 4AD 0.425287 0.706667
172 NSS 0.425287 0.630952
173 AMO 0.425287 0.716216
174 A3R 0.425287 0.697368
175 A1R 0.425287 0.697368
176 ADQ 0.425287 0.726027
177 2A5 0.425 0.68
178 SXZ 0.422222 0.75
179 ME8 0.422222 0.683544
180 PTJ 0.422222 0.710526
181 TXA 0.422222 0.739726
182 BIS 0.422222 0.697368
183 9K8 0.422222 0.627907
184 3OD 0.422222 0.75
185 00A 0.420455 0.697368
186 AHX 0.420455 0.688312
187 DLL 0.420455 0.736111
188 ATR 0.419753 0.742857
189 7D4 0.417722 0.666667
190 TAD 0.416667 0.679487
191 ADP BMA 0.41573 0.726027
192 A6D 0.41573 0.716216
193 3UK 0.41573 0.726027
194 AFX 0.411765 0.716418
195 26A 0.411765 0.787879
196 P5A 0.411111 0.602273
197 PR8 0.411111 0.670886
198 B5V 0.411111 0.716216
199 A A 0.411111 0.746479
200 KAA 0.411111 0.609195
201 LAD 0.411111 0.679487
202 J4G 0.411111 0.706667
203 V3L 0.409639 0.746479
204 B5M 0.408602 0.72973
205 YAP 0.408602 0.706667
206 B5Y 0.408602 0.72973
207 0XU 0.407407 0.828125
208 JB6 0.406593 0.697368
209 FYA 0.406593 0.736111
210 NB8 0.406593 0.688312
211 YSA 0.404255 0.630952
212 ZDA 0.402439 0.742857
213 25L 0.402174 0.736111
214 TYR AMP 0.4 0.706667
215 101 0.4 0.708333
216 A A A 0.4 0.736111
217 4UV 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: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3ci3.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
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: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 3ci3.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
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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