Receptor
PDB id Resolution Class Description Source Keywords
2PXH 1.97 Å EC: 6.1.1.1 CRYSTAL STRUCTURE OF A BIPYRIDYLALANYL-TRNA SYNTHETASE METHANOCALDOCOCCUS JANNASCHII METAL CHELATOR BIPYRIDYLALANINE UNNATURAL AMINO ACID LIGA
Ref.: A GENETICALLY ENCODED BIDENTATE, METAL-BINDING AMIN ANGEW.CHEM.INT.ED.ENGL. V. 46 9239 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BP5 A:308;
 Valid;
 none;
 submit data
243.261 C13 H13 N3 O2 c1ccn...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5N5U 1.6 Å EC: 6.1.1.1 STRUCTURE OF P-BORONOPHENYLALANYL TRNA SYNTHETASE IN COMPLEX BORONOPHENYLALANINE AND ADENOSINE MONOPHOSPHATE METHANOCALDOCOCCUS JANNASCHII (STRAIN 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) AMINOACYLATION LIGASE NON-NATURAL AMINO ACID SYNTHETIC BI
Ref.: STRUCTURAL BASIS FOR THE SPECIFIC COTRANSLATIONAL INCORPORATION OF P-BORONOPHENYLALANINE INTO BIOSYNT PROTEINS. BIOCHEMISTRY V. 57 2597 2018
Members (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 13 families.
1 4NX2 - 2LT C9 H9 Cl2 N O3 c1c(cc(c(c....
2 3QE4 - 4CF C10 H10 N2 O2 c1cc(ccc1C....
3 4NDA - NIY C9 H10 N2 O5 c1cc(c(cc1....
4 3D6V - TFQ C11 H12 F3 N O2 c1cc(ccc1C....
5 2AG6 - 4BF C9 H10 Br N O2 c1cc(ccc1C....
6 3D6U - T11 C11 H12 F3 N3 O2 c1cc(ccc1C....
7 4PBT - 2LQ C18 H24 N2 O3 c1cc(ccc1C....
8 5N5U - AMP C10 H14 N5 O7 P c1nc(c2c(n....
9 2HGZ - PBF C16 H15 N O3 c1ccc(cc1)....
10 4PBR - 2L7 C13 H17 Br N2 O3 CC(C)(C(=O....
11 5L7P - BUU C16 H16 N2 O6 c1ccc(c(c1....
12 2PXH - BP5 C13 H13 N3 O2 c1ccnc(c1)....
13 5NSF - 96Z C13 H15 N O2 C1C=CC2=CC....
14 3N2Y - TEF C10 H11 N5 O2 c1cc(ccc1C....
15 6WRN - NIY C9 H10 N2 O5 c1cc(c(cc1....
16 1ZH6 - 4AF C11 H13 N O3 CC(=O)c1cc....
17 4PBS - 2L7 C13 H17 Br N2 O3 CC(C)(C(=O....
18 6WRK - NIY C9 H10 N2 O5 c1cc(c(cc1....
19 1ZH0 - NAL C13 H13 N O2 c1ccc2cc(c....
20 6WRQ - NIY C9 H10 N2 O5 c1cc(c(cc1....
21 6WRT - NIY C9 H10 N2 O5 c1cc(c(cc1....
70% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 2CYB - TYR C9 H11 N O3 c1cc(ccc1C....
2 4NX2 - 2LT C9 H9 Cl2 N O3 c1c(cc(c(c....
3 3QE4 - 4CF C10 H10 N2 O2 c1cc(ccc1C....
4 4NDA - NIY C9 H10 N2 O5 c1cc(c(cc1....
5 3D6V - TFQ C11 H12 F3 N O2 c1cc(ccc1C....
6 2AG6 - 4BF C9 H10 Br N O2 c1cc(ccc1C....
7 3D6U - T11 C11 H12 F3 N3 O2 c1cc(ccc1C....
8 4PBT - 2LQ C18 H24 N2 O3 c1cc(ccc1C....
9 5N5U - AMP C10 H14 N5 O7 P c1nc(c2c(n....
10 2HGZ - PBF C16 H15 N O3 c1ccc(cc1)....
11 4PBR - 2L7 C13 H17 Br N2 O3 CC(C)(C(=O....
12 5L7P - BUU C16 H16 N2 O6 c1ccc(c(c1....
13 2PXH - BP5 C13 H13 N3 O2 c1ccnc(c1)....
14 5NSF - 96Z C13 H15 N O2 C1C=CC2=CC....
15 3N2Y - TEF C10 H11 N5 O2 c1cc(ccc1C....
16 6WRN - NIY C9 H10 N2 O5 c1cc(c(cc1....
17 1ZH6 - 4AF C11 H13 N O3 CC(=O)c1cc....
18 4PBS - 2L7 C13 H17 Br N2 O3 CC(C)(C(=O....
19 6WRK - NIY C9 H10 N2 O5 c1cc(c(cc1....
20 1ZH0 - NAL C13 H13 N O2 c1ccc2cc(c....
21 6WRQ - NIY C9 H10 N2 O5 c1cc(c(cc1....
22 6WRT - NIY C9 H10 N2 O5 c1cc(c(cc1....
50% Homology Family (27)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2CYB - TYR C9 H11 N O3 c1cc(ccc1C....
2 4NX2 - 2LT C9 H9 Cl2 N O3 c1c(cc(c(c....
3 3QE4 - 4CF C10 H10 N2 O2 c1cc(ccc1C....
4 4NDA - NIY C9 H10 N2 O5 c1cc(c(cc1....
5 3D6V - TFQ C11 H12 F3 N O2 c1cc(ccc1C....
6 2AG6 - 4BF C9 H10 Br N O2 c1cc(ccc1C....
7 3D6U - T11 C11 H12 F3 N3 O2 c1cc(ccc1C....
8 4PBT - 2LQ C18 H24 N2 O3 c1cc(ccc1C....
9 5N5U - AMP C10 H14 N5 O7 P c1nc(c2c(n....
10 2HGZ - PBF C16 H15 N O3 c1ccc(cc1)....
11 4PBR - 2L7 C13 H17 Br N2 O3 CC(C)(C(=O....
12 5L7P - BUU C16 H16 N2 O6 c1ccc(c(c1....
13 2PXH - BP5 C13 H13 N3 O2 c1ccnc(c1)....
14 5NSF - 96Z C13 H15 N O2 C1C=CC2=CC....
15 3N2Y - TEF C10 H11 N5 O2 c1cc(ccc1C....
16 6WRN - NIY C9 H10 N2 O5 c1cc(c(cc1....
17 1ZH6 - 4AF C11 H13 N O3 CC(=O)c1cc....
18 4PBS - 2L7 C13 H17 Br N2 O3 CC(C)(C(=O....
19 6WRK - NIY C9 H10 N2 O5 c1cc(c(cc1....
20 1ZH0 - NAL C13 H13 N O2 c1ccc2cc(c....
21 6WRQ - NIY C9 H10 N2 O5 c1cc(c(cc1....
22 6WRT - NIY C9 H10 N2 O5 c1cc(c(cc1....
23 2CYC - TYR C9 H11 N O3 c1cc(ccc1C....
24 1Q11 - TYE C9 H13 N O2 c1cc(ccc1C....
25 5THH - TYR C9 H11 N O3 c1cc(ccc1C....
26 3VGJ - TYR AMP n/a n/a
27 2J5B - TYE C9 H13 N O2 c1cc(ccc1C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: BP5; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 BP5 1 1
2 DPN 0.433962 0.6875
3 PHE 0.433962 0.6875
4 NAL 0.403226 0.705882
Similar Ligands (3D)
Ligand no: 1; Ligand: BP5; Similar ligands found: 119
No: Ligand Similarity coefficient
1 TEF 0.9634
2 PB2 0.9455
3 SYD 0.9412
4 D26 0.9243
5 3K1 0.9206
6 KOH 0.9204
7 5TT 0.9199
8 HPK 0.9185
9 RF2 0.9182
10 BFL 0.9145
11 7KE 0.9144
12 CT0 0.9126
13 PTR 0.9118
14 2L7 0.9115
15 LC1 0.9112
16 MKN 0.9110
17 Z3R 0.9107
18 CIU 0.9088
19 D25 0.9088
20 39R 0.9083
21 HDI 0.9071
22 S45 0.9067
23 4VC 0.9060
24 2OX 0.9045
25 CR4 0.9044
26 L02 0.9038
27 1OT 0.9027
28 BMZ 0.9023
29 135 0.9022
30 NNF 0.9013
31 124 0.9002
32 120 0.8999
33 E42 0.8991
34 801 0.8986
35 J2P 0.8974
36 F91 0.8964
37 122 0.8951
38 J2N 0.8949
39 6NF 0.8947
40 TFX 0.8941
41 0LA 0.8939
42 C0V 0.8931
43 SJR 0.8930
44 4UE 0.8915
45 Y27 0.8912
46 20P 0.8906
47 0MB 0.8906
48 90M 0.8901
49 J3B 0.8888
50 TFQ 0.8872
51 23M 0.8871
52 6DH 0.8871
53 90G 0.8864
54 HAU 0.8857
55 A5W 0.8856
56 1CE 0.8855
57 121 0.8854
58 651 0.8853
59 LIT 0.8851
60 5ET 0.8844
61 BCE 0.8839
62 M5A 0.8835
63 1GV 0.8834
64 REG 0.8832
65 20N 0.8822
66 4ZW 0.8814
67 N0E 0.8814
68 22M 0.8813
69 MI2 0.8809
70 FTK 0.8808
71 5OD 0.8800
72 856 0.8798
73 35K 0.8797
74 F5N 0.8797
75 AZB 0.8793
76 AD6 0.8790
77 1Q1 0.8789
78 521 0.8783
79 ZTW 0.8779
80 ZUF 0.8778
81 D9Q 0.8778
82 109 0.8777
83 GJG 0.8776
84 47X 0.8774
85 RKY 0.8766
86 246 0.8761
87 7N8 0.8760
88 ESJ 0.8744
89 AT2 0.8742
90 HTK 0.8741
91 5OA 0.8737
92 U55 0.8731
93 F41 0.8727
94 1PB 0.8719
95 JXA 0.8719
96 0NJ 0.8717
97 5EZ 0.8713
98 K4T 0.8709
99 HMO 0.8707
100 4UM 0.8707
101 397 0.8706
102 M25 0.8700
103 A8D 0.8692
104 JP5 0.8681
105 BOS 0.8674
106 077 0.8664
107 K3T 0.8656
108 SQG 0.8646
109 JVB 0.8643
110 A11 0.8639
111 EAA 0.8631
112 VGV 0.8627
113 GJW 0.8617
114 GBJ 0.8614
115 HMX 0.8601
116 5XM 0.8600
117 3G3 0.8587
118 BON 0.8573
119 789 0.8512
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5N5U; Ligand: AMP; 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: 5n5u.bio1) has 50 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5N5U; Ligand: AMP; 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: 5n5u.bio1) has 50 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5N5U; Ligand: 7N8; 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: 5n5u.bio1) has 39 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5N5U; Ligand: 7N8; 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: 5n5u.bio1) has 39 residues
No: Leader PDB Ligand Sequence Similarity
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