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Receptor
PDB id Resolution Class Description Source Keywords
3NUB 1.9 Å EC: 2.-.-.- WBPE, AN AMINOTRANSFERASE FROM PSEUDOMONAS AERUGINOSA INVOLV ANTIGEN ASSEMBLY IN COMPLEX WITH PRODUCT AS THE EXTERNAL AL PSEUDOMONAS AERUGINOSA DOMAIN-SWAPPED BETA HAIRPIN AMINOTRANSFERASE EXTERNAL ALDIPLP PMP UDP-GLCNAC(3NH2)A LIPOPOLYSACCHARIDE PSEUDOMONAAERUGINOSA O-ANTIGEN B-BAND TRANSFERASE
Ref.: STRUCTURAL ANALYSIS OF WBPE FROM PSEUDOMONAS AERUGI PAO1: A NUCLEOTIDE SUGAR AMINOTRANSFERASE INVOLVED O-ANTIGEN ASSEMBLY BIOCHEMISTRY V. 49 7227 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:360;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
SO4 A:361;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
UD0 A:400;
B:400;
Valid;
Valid;
none;
none;
submit data
849.479 C25 H34 N5 O22 P3 Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3NUB 1.9 Å EC: 2.-.-.- WBPE, AN AMINOTRANSFERASE FROM PSEUDOMONAS AERUGINOSA INVOLV ANTIGEN ASSEMBLY IN COMPLEX WITH PRODUCT AS THE EXTERNAL AL PSEUDOMONAS AERUGINOSA DOMAIN-SWAPPED BETA HAIRPIN AMINOTRANSFERASE EXTERNAL ALDIPLP PMP UDP-GLCNAC(3NH2)A LIPOPOLYSACCHARIDE PSEUDOMONAAERUGINOSA O-ANTIGEN B-BAND TRANSFERASE
Ref.: STRUCTURAL ANALYSIS OF WBPE FROM PSEUDOMONAS AERUGI PAO1: A NUCLEOTIDE SUGAR AMINOTRANSFERASE INVOLVED O-ANTIGEN ASSEMBLY BIOCHEMISTRY V. 49 7227 2010
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 269 families.
1 3NU7 - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
2 3NUB - UD0 C25 H34 N5 O22 P3 Cc1c(c(c(c....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 237 families.
1 3NU7 - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
2 3NUB - UD0 C25 H34 N5 O22 P3 Cc1c(c(c(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: UD0; Similar ligands found: 55
No: Ligand ECFP6 Tc MDL keys Tc
1 UD0 1 1
2 4RA 0.792593 0.987013
3 HP7 0.615385 0.87013
4 MJZ 0.610687 0.871795
5 EEB 0.553191 0.860759
6 UD2 0.552239 0.858974
7 UD1 0.552239 0.858974
8 F5G 0.547445 0.883117
9 UGA 0.546154 0.857143
10 UGB 0.546154 0.857143
11 EPZ 0.546099 0.871795
12 2QR 0.546053 0.879518
13 EPU 0.542253 0.8375
14 F5P 0.536232 0.871795
15 UD4 0.536232 0.871795
16 UD7 0.532847 0.883117
17 UDZ 0.521127 0.819277
18 UMA 0.513333 0.871795
19 U20 0.512987 0.781609
20 U21 0.512987 0.781609
21 UFM 0.484848 0.846154
22 UPG 0.484848 0.846154
23 GUD 0.484848 0.846154
24 GDU 0.484848 0.846154
25 U22 0.484076 0.784091
26 TQP 0.477987 0.903614
27 7SG 0.477987 0.903614
28 T4K 0.475 0.915663
29 T5K 0.475 0.915663
30 U2F 0.474074 0.804878
31 UFG 0.474074 0.804878
32 UPF 0.474074 0.804878
33 UAG 0.472727 0.851852
34 HWU 0.472222 0.814815
35 12V 0.472222 0.814815
36 UDM 0.471429 0.825
37 USQ 0.467153 0.75
38 PMP UD1 0.463415 0.86747
39 UDX 0.463235 0.846154
40 UAD 0.463235 0.846154
41 UML 0.457143 0.802326
42 G3N 0.453237 0.825
43 UNP 0.446154 0.822785
44 UTP 0.445312 0.844156
45 UDP 0.444444 0.844156
46 660 0.441176 0.8125
47 URM 0.441176 0.8125
48 3UC 0.429577 0.804878
49 IUG 0.426667 0.802326
50 O1G 0.419118 0.766234
51 UDH 0.413043 0.744186
52 U 0.408 0.831169
53 U5P 0.408 0.831169
54 UPU 0.407407 0.820513
55 UPP 0.402878 0.87013
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3NUB; Ligand: UD0; Similar sites found with APoc: 135
This union binding pocket(no: 1) in the query (biounit: 3nub.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 2CJH AKG 1.11421
2 3FQ8 PMP 1.39276
3 3ZRR PXG 1.67131
4 2OAT PFM 1.67131
5 6DND PLP 2.22841
6 3A8U PLP 2.22841
7 4UHO PLP 2.22841
8 4B98 PXG 2.22841
9 1UU1 PMP HSA 2.38806
10 5LXB 7A9 2.47934
11 4BA5 PXG 2.50696
12 2HOX P1T 2.50696
13 3R75 PYR 2.50696
14 1IXE CIT 2.50696
15 4RM0 FUC NAG GAL 2.53165
16 5TDC NMM ILE PHE SER 2.63158
17 2FYF PLP 2.76382
18 2R2N PMP 2.78552
19 1OXO IK2 2.78552
20 4ADC PLP 2.78552
21 2R2N KYN 2.78552
22 5KGS 6SR 3.06407
23 5BU2 AMP 3.06407
24 1VJO PLP 3.34262
25 1MLY ACZ PLP 3.34262
26 1LC8 33P 3.34262
27 4JE5 PMP 3.34262
28 4JE5 PLP 3.34262
29 2PEL LBT 3.38983
30 1KW6 BPY 3.42466
31 3KB6 LAC 3.59281
32 4ZSY RW2 3.62117
33 6CZY PMP 3.62117
34 1JS3 PLP 142 3.62117
35 6FYQ PLP 3.89972
36 4HVK PMP 3.89972
37 1M32 PLP 3.89972
38 1WYV PLP AOA 3.89972
39 4R8L ASP 3.89972
40 5DNC ASN 3.89972
41 1H74 ILE 4.05405
42 3I7S PYR 4.10959
43 1SFF IK2 4.17827
44 5G09 6DF 4.17827
45 6MVU K4V 4.17827
46 5H3A UMP 4.24028
47 5WYF ILP 4.45682
48 3EI9 PL6 4.45682
49 2ZYJ PGU 4.45682
50 3A70 NPO 4.45682
51 3PD6 PMP 4.73538
52 3PDB PMP 4.73538
53 2Z9V PXM 4.73538
54 5EGH PC 4.73538
55 4RKC PMP 5.01393
56 5W19 9TD 5.29248
57 1TOI HCI 5.29248
58 5DDW 5B6 5.29248
59 5M3Z PLP 5.84958
60 5M3Z PY6 5.84958
61 5M3Z NLE 5.84958
62 4JLZ UTP 6.12813
63 1ZC9 PMP 6.40669
64 2OG2 MLI 6.40669
65 4IY7 0JO 6.40669
66 4IYO 0JO 6.40669
67 4IY7 KOU 6.40669
68 1K4M CIT 6.57277
69 1AJS PLA 6.68524
70 3CQ5 PMP 6.68524
71 5G4J EXT 6.68524
72 5YKT PMP 6.96379
73 5LA1 XYP 6.96379
74 5V8E CIT 7.11974
75 2P1E LAC 7.24234
76 6CD1 PLG 7.24234
77 6CD1 PLS 7.24234
78 2BHZ MAL 7.24234
79 5Z21 OXM 7.26257
80 4FL0 PLP 7.52089
81 1U26 IHS 8.01187
82 4UOX PLP 8.07799
83 4UOX PUT 8.07799
84 4UOX PLP PUT 8.07799
85 2RDK MAN MAN 8.25688
86 2DVZ GLU 8.28025
87 4LNL 2BO 8.40841
88 4LNL 2BK 8.40841
89 4LNL PLG 8.40841
90 1ELU CSS 8.46154
91 1ELU PDA 8.46154
92 1GDE GLU PLP 8.6351
93 5VEQ PMP 8.91365
94 5TXR PLP 10.0279
95 2VPY PCI 10.2767
96 2R5C C6P 10.3064
97 2R5E QLP 10.3064
98 4RJD TFP 10.6061
99 1W6F ISZ 10.7914
100 4R5Z PMP 10.8635
101 1E5F PLP 11.1421
102 3BS8 PMP 11.1421
103 4N7C AEF 11.3636
104 3VP6 HLD 12.5348
105 1PMO PLR 12.8134
106 5IWQ PLP 12.8134
107 2TPL HPP 12.8134
108 6ECG PM9 12.8134
109 5LY1 PPI 12.8134
110 4WGF HX2 13.6585
111 1U08 PLP 13.9276
112 1DFO PLG 14.2061
113 2WK9 PLG 14.2061
114 2WK9 PLP 14.2061
115 1GCK ASP PLP 15.8774
116 5X30 4LM 16.7131
117 5X30 7XF 16.7131
118 5X2Z 3LM 16.7131
119 1LW4 TLP 16.7147
120 1LW4 PLP 16.7147
121 1FC4 AKB PLP 17.2702
122 3ITJ CIT 17.4556
123 2ZC0 PMP 18.1059
124 3WGC PLG 18.4751
125 1DJ9 KAM 19.4986
126 4WXG 2BO 20.6128
127 3B8X G4M 34.2618
128 5K8B PDG 34.8189
129 5W71 PLP 38.4401
130 5W71 9YM 38.4401
131 5W70 9YM 38.9972
132 1B9I PXG 38.9972
133 6EWR PMP 42.8969
134 4ZAH T5K 43.454
135 2PO3 T4K 48.468
Pocket No.: 2; Query (leader) PDB : 3NUB; Ligand: UD0; Similar sites found with APoc: 41
This union binding pocket(no: 2) in the query (biounit: 3nub.bio1) has 32 residues
No: Leader PDB Ligand Sequence Similarity
1 4X9D U5P None
2 1YZG GDP 1.11732
3 4XDA ADP 1.2945
4 4AK7 47N 1.67131
5 2VWT PYR 1.87266
6 4BTV RB3 2.61628
7 2AWN ADP 2.78552
8 1P7T PYR 2.78552
9 1ONX ASP 2.78552
10 2V5K OXM 3.13589
11 2GNM MAN 3.1746
12 1M5W DXP 3.29218
13 4B5W PYR 3.51562
14 4E1O PLP PVH 3.62117
15 2Y6P CTP 3.84615
16 5OCQ CIT 3.85965
17 3CV2 OXL 3.89972
18 1R87 XYP XYP 3.89972
19 6BE0 COA 3.97351
20 6HQD SRT 4.45682
21 2A9W UMP 4.54545
22 4L80 OXL 4.5977
23 4L9Z OXL 4.71976
24 5Z3I ADE 4.90566
25 5ZCT ANP 5.22876
26 3R7F CP 5.26316
27 1J1R ADE 5.74713
28 3B9Z CO2 5.84958
29 1CT9 AMP 5.84958
30 5ZYN SIN 5.84958
31 5GLN XYP XYP XYP 6.10465
32 2ZUX RAM 6.68524
33 1Q19 SSC 7.24234
34 1G6H ADP 7.393
35 3WUC GLC GAL 8.0292
36 1I7Q PYR 8.35655
37 1IZC PYR 9.14454
38 5WHU SIA 9.39597
39 4KTP BGC 9.47075
40 5E13 5J9 9.93789
41 4JNJ BTN 10.4348
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