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Receptor
PDB id Resolution Class Description Source Keywords
3BN1 1.8 Å EC: 7.-.-.- CRYSTAL STRUCTURE OF GDP-PEROSAMINE SYNTHASE CAULOBACTER CRESCENTUS PEROSAMINE ASPARTATE AMINOTRANSFERASE DEOXYSUGAR O-ANTIGETRANSFERASE
Ref.: GDP-PEROSAMINE SYNTHASE: STRUCTURAL ANALYSIS AND PR OF A NOVEL TRIDEOXYSUGAR BIOCHEMISTRY V. 47 2833 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT A:372;
C:372;
D:372;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
59.044 C2 H3 O2 CC(=O...
AKG A:374;
Valid;
none;
submit data
146.098 C5 H6 O5 C(CC(...
NA A:373;
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
3DR4 1.6 Å EC: 7.-.-.- GDP-PEROSAMINE SYNTHASE K186A MUTANT FROM CAULOBACTER CRESCENTUS WITH BOUND SUGAR LIGAND CAULOBACTER CRESCENTUS PEROSAMINE DEOXYSUGAR PYRIDOXAL PHOSPHATE ASPARTATE AMINOTRANSFERASE O-ANTIGEN
Ref.: ACCOMMODATION OF GDP-LINKED SUGARS IN THE ACTIVE SITE OF GDP-PEROSAMINE SYNTHASE BIOCHEMISTRY V. 47 10685 2008
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 293 families.
1 3BN1 - AKG C5 H6 O5 C(CC(=O)O)....
2 3DR4 - G4M C24 H36 N7 O19 P3 Cc1c(c(c(c....
3 3DR7 - GPD C16 H26 N6 O13 P2 C[C@@H]1[C....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 250 families.
1 3BN1 - AKG C5 H6 O5 C(CC(=O)O)....
2 3DR4 - G4M C24 H36 N7 O19 P3 Cc1c(c(c(c....
3 3DR7 - GPD C16 H26 N6 O13 P2 C[C@@H]1[C....
50% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 187 families.
1 5U21 - TQP C24 H35 N4 O19 P3 Cc1c(c(c(c....
2 5U23 - TQP C24 H35 N4 O19 P3 Cc1c(c(c(c....
3 5U24 - 7SG C24 H35 N4 O19 P3 Cc1c(c(c(c....
4 1O69 - X04 C8 H11 N2 O6 P Cc1c(c(c(c....
5 1O61 - PLP C8 H10 N O6 P Cc1c(c(c(c....
6 3FRK - TQP C24 H35 N4 O19 P3 Cc1c(c(c(c....
7 3NU7 - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
8 3NUB - UD0 C25 H34 N5 O22 P3 Cc1c(c(c(c....
9 3BN1 - AKG C5 H6 O5 C(CC(=O)O)....
10 3DR4 - G4M C24 H36 N7 O19 P3 Cc1c(c(c(c....
11 3DR7 - GPD C16 H26 N6 O13 P2 C[C@@H]1[C....
12 2OGA - PGU C13 H19 N2 O9 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: AKG; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 AKG 1 1
2 SIN 0.526316 0.833333
3 OOG 0.5 0.947368
4 69O 0.458333 0.714286
5 2IT 0.423077 0.615385
6 SHF 0.416667 0.666667
7 3PY 0.409091 0.652174
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3DR4; Ligand: G4M; Similar sites found with APoc: 168
This union binding pocket(no: 1) in the query (biounit: 3dr4.bio1) has 37 residues
No: Leader PDB Ligand Sequence Similarity
1 1Z0N BCD None
2 6MVU K4V 1.27877
3 4JE5 PMP 1.27877
4 4V15 PLP 1.31926
5 1CL2 PPG 1.53453
6 3EI9 PL6 1.79028
7 6CD1 PLS 1.79028
8 6CD1 PLG 1.79028
9 5IWQ PLP 1.79028
10 5J75 6GQ 1.89394
11 4ZM4 PLP 2.04604
12 1CT9 AMP 2.04604
13 4ZM4 P3B 2.04604
14 3K4Q IHS 2.04604
15 2MPR BGC GLC GLC 2.04604
16 1HGX 5GP 2.18579
17 3BWN PMP 2.30179
18 5DDW 5B6 2.30179
19 4ADC PLP 2.30179
20 3BWN PMP PHE 2.30179
21 6BYF CIT 2.35294
22 4X1Z FUC GAL NDG 2.40964
23 1LC8 33P 2.47253
24 5LV1 78T 2.5
25 3BS8 PMP 2.55754
26 1VJO PLP 2.55754
27 3I4X DST 2.55754
28 1FC4 AKB PLP 2.55754
29 5YKT PMP 2.8133
30 1MLY ACZ PLP 2.8133
31 1WYV PLP AOA 2.8133
32 5H3A UMP 2.82686
33 1MZV AMP 2.97872
34 2CJH AKG 3.06905
35 4RKC PMP 3.06905
36 1DFO PLG 3.06905
37 2C5S AMP 3.06905
38 5WS9 OXL 3.06905
39 1YFS ALA 3.06905
40 1H8S AIC 3.06905
41 2JBH 5GP 3.11111
42 2HVW DCP 3.26087
43 1M32 PLP 3.27869
44 1UU1 PMP HSA 3.28358
45 1M5W DXP 3.29218
46 4BA5 PXG 3.32481
47 6DND PLP 3.32481
48 4UOX PLP 3.32481
49 1PMO PLR 3.32481
50 4UOX PUT 3.32481
51 4FL0 PLP 3.32481
52 4UOX PLP PUT 3.32481
53 5J32 IPM 3.32481
54 2YLN CYS 3.53357
55 1E5F PLP 3.58056
56 3FQ8 PMP 3.58056
57 2RG0 CBI 3.58056
58 1AJS PLA 3.64078
59 5ZMY TAR 3.82166
60 5G09 6DF 3.83632
61 2WZF BGC 3.83632
62 5W19 9TD 4.09207
63 5UFF 8B7 4.16667
64 4WOH 4NP 4.21687
65 2Z77 HE7 4.31655
66 3CQ5 PMP 4.34783
67 4P86 5GP 4.37158
68 3WGC PLG 4.39883
69 4UHO PLP 4.60358
70 1ZC9 PMP 4.60358
71 4B4Q A2G GAL NAG FUC GAL GLC 4.63576
72 2PEL LBT 4.66102
73 1VRP IOM 4.72441
74 4JCA CIT 4.79042
75 4KCT PYR 4.80962
76 2Z9V PXM 4.85933
77 4IP7 FLC 4.85933
78 1LRH NLA 4.90798
79 1SFF IK2 5.11509
80 4B98 PXG 5.11509
81 1U6R IOM 5.26316
82 3VP6 HLD 5.37084
83 3A8U PLP 5.6266
84 2X5F PLP 5.6266
85 1TZD ADP 5.6266
86 3JQ3 ADP 5.7377
87 5ME4 HP4 5.83942
88 4WOE 3S5 5.88235
89 5E58 CPZ 5.88235
90 1SDW IYT 6.05096
91 5M3Z PLP 6.13811
92 5M3Z PY6 6.13811
93 4IY7 KOU 6.13811
94 4IY7 0JO 6.13811
95 4IYO 0JO 6.13811
96 5M3Z NLE 6.13811
97 2CI5 HCS 6.33803
98 3P9T TCL 6.39269
99 4AOA IK2 6.39386
100 3BGD PM6 6.53846
101 5LXB 7A9 6.61157
102 6GN6 MAL 6.71141
103 3ZRR PXG 6.77083
104 4K79 GAL A2G 6.81818
105 4E3Q PMP 6.90537
106 6CBO DOW 7.16113
107 5ERM 210 7.16253
108 3H2K BOG 7.41688
109 6CZY PMP 7.45856
110 4R8L ASP 7.53247
111 3MBI HSX 7.66551
112 4ZSY RW2 7.67263
113 4HVK PMP 8.37696
114 3PDB PMP 8.4399
115 3PD6 PMP 8.4399
116 1TOI HCI 8.69565
117 2PS1 ORO 8.84956
118 1K4M CIT 9.38967
119 4M2K PLP 9.71867
120 6CBN OZY 9.71867
121 4MN3 ACE PHE ALA TYR M3L SER NH2 10.7143
122 2R2N PMP 10.7417
123 2R5E QLP 10.7417
124 2R5C C6P 10.7417
125 6FYQ PLP 10.9974
126 5VEQ PMP 11.509
127 4R5Z PMP 11.7166
128 4P83 U5P 12.0879
129 2OAT PFM 13.0435
130 1U08 PLP 13.4715
131 5X30 4LM 13.555
132 5X30 7XF 13.555
133 2ZC0 PMP 13.555
134 5X2Z 3LM 13.555
135 4RJD TFP 13.6364
136 1LOJ U 13.7931
137 4WXG 2BO 13.8107
138 2IMG MLT 13.9073
139 1DQN IMU 13.913
140 1GCK ASP PLP 14.026
141 5WYF ILP 14.3223
142 1XI9 PLP 14.578
143 1DJ9 KAM 15.8854
144 1ELU PDA 16.1538
145 1ELU CSS 16.1538
146 4LFL TG6 16.2791
147 5G4J EXT 16.8798
148 4FDU IHS 18.6701
149 4LNL PLG 20.7207
150 4LNL 2BK 20.7207
151 4LNL 2BO 20.7207
152 1GDE GLU PLP 21.8509
153 1LW4 PLP 22.2506
154 1LW4 TLP 22.2506
155 5TXR PLP 24.0409
156 1C4Q GLA GAL BGC 27.5362
157 6ECG PM9 28.9003
158 2TPL HPP 28.9003
159 1A5V Y3 29.1139
160 5K8B PDG 32.9923
161 1B9I PXG 44.8454
162 3B8X G4M 47.4359
163 4ZAH T5K 47.8261
164 5W71 PLP 48.0818
165 5W70 9YM 48.0818
166 5W71 9YM 48.0818
167 4K2M O1G 48.3376
168 2FNU PMP UD1 49.8667
Pocket No.: 2; Query (leader) PDB : 3DR4; Ligand: G4M; Similar sites found with APoc: 39
This union binding pocket(no: 2) in the query (biounit: 3dr4.bio1) has 39 residues
No: Leader PDB Ligand Sequence Similarity
1 2HOX P1T 1.27877
2 4K10 NI9 1.38122
3 4XZ6 TMO 1.47493
4 4UOZ GLA 1.79028
5 5EGH PC 1.79028
6 5KDS A2G THR ALA PRO GLY GLY NAG SIA 1.79028
7 3AI8 HNQ 2.34375
8 4EIL CB3 2.55754
9 2GWH PCI 2.68456
10 2FYF PLP 2.76382
11 4E1O PLP PVH 2.8133
12 5H3A D16 2.82686
13 1DDU DDU 3.01887
14 1JG0 DDT 3.0303
15 4NM5 ADP 3.18302
16 2I6A 5I5 3.18841
17 5CDH TLA 3.27381
18 2QUN FUD 3.44828
19 3R75 PYR 3.58056
20 4MO4 ACP 3.58056
21 5NN6 MIG 3.83632
22 6FFI D8B 3.83632
23 3B9Z CO2 3.86598
24 2DVX 23A 4.28135
25 2R68 SUP 4.60358
26 2PEL LAT 4.66102
27 3GLC R5P 4.74576
28 1U6R ADP 5.26316
29 3ACC 5GP 5.52486
30 4SGA ACE PRO ALA PRO PHE 5.52486
31 3I7V ATP 5.97015
32 1SQL GUN 6.16438
33 4TYO 39X 7.31707
34 3DGY 2GP 8.24742
35 4DS8 A8S 8.45481
36 3B8I OXL 10.1045
37 1RGE 2GP 10.4167
38 1Y7P RIP 11.6592
39 5Z84 PEK 22.0339
Pocket No.: 3; Query (leader) PDB : 3DR4; Ligand: G4M; Similar sites found with APoc: 30
This union binding pocket(no: 3) in the query (biounit: 3dr4.bio2) has 39 residues
No: Leader PDB Ligand Sequence Similarity
1 1PS9 FMN 2.04604
2 4RZB NFQ 2.42826
3 3KRO IPE 2.55474
4 5KWW 6YA 2.55754
5 3HQP OXL 2.55754
6 4ISK UMP 3.0303
7 3K8D CTP 3.0303
8 3ITJ CIT 3.5503
9 1H8P PC 3.66972
10 3AI3 SOL 3.80228
11 5BXA MAN 3.83632
12 3I7S PYR 4.34783
13 4GYS MLI 4.34783
14 3B99 U51 4.34783
15 1A99 PUT 4.36047
16 3ROE THM 5.28302
17 3BMO AX4 6.25
18 3JQG AX6 6.25
19 3BMQ AX5 6.25
20 3JQ7 DX2 6.25
21 2ZYJ PGU 6.54912
22 4DN8 BMA 7.05128
23 6AM8 TRP 7.41688
24 3TTY GLA 7.92839
25 4HIA FMN 7.95455
26 4B1M FRU FRU 8.10811
27 2D3Y DU 8.21918
28 5JNW 6LJ 8.80503
29 5GGN LEC 10.3659
30 3MN5 LAB 15.7895
Pocket No.: 4; Query (leader) PDB : 3DR4; Ligand: G4M; Similar sites found with APoc: 10
This union binding pocket(no: 4) in the query (biounit: 3dr4.bio2) has 36 residues
No: Leader PDB Ligand Sequence Similarity
1 1PSC EBP 2.19178
2 5VJN ADE 2.6738
3 2VDV SAM 2.84553
4 6CDZ UMP 3.04183
5 5WS9 ATP 3.06905
6 2JKY 5GP 3.28639
7 1NSZ GLC 3.45821
8 6GVZ CHO 3.60656
9 1A05 IPM 6.42458
10 1B0U ATP 9.92366
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