Receptor
PDB id Resolution Class Description Source Keywords
5TFZ 2.2 Å EC: 4.-.-.- CRYSTAL STRUCTURE OF THE DIMETHYLSULFONIOPROPIONATE (DMSP) L COMPLEXED WITH NICKEL AND DIACRYLATE PELAGIBACTER UBIQUE (STRAIN HTCC1062) DMSP LYASE CUPIN NICKEL DEPENDENT METAL BINDING OXIDORED
Ref.: STRUCTURAL AND BIOCHEMICAL INSIGHTS INTO DIMETHYLSULFONIOPROPIONATE CLEAVAGE BY COFACTOR-BOU FROM THE PROLIFIC MARINE BACTERIUM PELAGIBACTER. BIOCHEMISTRY V. 56 2873 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
7BC B:205;
A:202;
Valid;
Valid;
none;
none;
submit data
144.125 C6 H8 O4 C=CC(...
PEG B:202;
B:201;
B:203;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
106.12 C4 H10 O3 C(COC...
NI A:201;
B:204;
Part of Protein;
Part of Protein;
none;
none;
submit data
58.693 Ni [Ni+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5TFZ 2.2 Å EC: 4.-.-.- CRYSTAL STRUCTURE OF THE DIMETHYLSULFONIOPROPIONATE (DMSP) L COMPLEXED WITH NICKEL AND DIACRYLATE PELAGIBACTER UBIQUE (STRAIN HTCC1062) DMSP LYASE CUPIN NICKEL DEPENDENT METAL BINDING OXIDORED
Ref.: STRUCTURAL AND BIOCHEMICAL INSIGHTS INTO DIMETHYLSULFONIOPROPIONATE CLEAVAGE BY COFACTOR-BOU FROM THE PROLIFIC MARINE BACTERIUM PELAGIBACTER. BIOCHEMISTRY V. 56 2873 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 38 families.
1 5TFZ - 7BC C6 H8 O4 C=CC(=O)OC....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 35 families.
1 5TFZ - 7BC C6 H8 O4 C=CC(=O)OC....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 27 families.
1 5TFZ - 7BC C6 H8 O4 C=CC(=O)OC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 7BC; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 7BC 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5TFZ; Ligand: 7BC; Similar sites found: 140
This union binding pocket(no: 1) in the query (biounit: 5tfz.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4AZP A9M 0.006627 0.43212 None
2 3SAO NKN 0.004782 0.4258 None
3 4WN5 MVC 0.01033 0.42077 None
4 5OO5 UUA 0.008162 0.41664 None
5 3AJH BL3 0.01316 0.4103 None
6 2XOM GAL GAL GAL 0.0002918 0.40266 1.33333
7 5DKK FMN 0.01872 0.40268 1.37931
8 4R38 RBF 0.01002 0.41801 1.42857
9 5BU3 4W9 0.001385 0.46277 2
10 4OCT AKG 0.0006007 0.45225 2
11 4NPL AKG 0.0008822 0.43732 2
12 4HIA FMN 0.01976 0.42066 2
13 3AVR OGA 0.0001853 0.49596 2.66667
14 3AVS OGA 0.0004921 0.46525 2.66667
15 5DQ8 FLF 0.0191 0.41688 2.66667
16 1IIU RTL 0.01205 0.41574 2.66667
17 1MDC PLM 0.01531 0.41213 3.0303
18 5HV0 AKG 0.00004661 0.52346 3.33333
19 4IGQ THR M3L GLN 0.001952 0.45139 3.33333
20 4IGQ OGA 0.00007531 0.43679 3.33333
21 4P7X AKG 0.004509 0.43138 3.33333
22 4P7X YCP 0.004509 0.43138 3.33333
23 1NYW DAU 0.007699 0.42187 3.33333
24 4Q0L V14 0.03125 0.40067 3.33333
25 2RDQ AKG 0.0004558 0.48689 4
26 1ZB6 GST 0.00194 0.46697 4
27 5FWJ MMK 0.0006242 0.46035 4
28 5LUN ARG 0.006542 0.4355 4
29 5LUN OGA 0.00213 0.42958 4
30 1ZB6 DIN 0.01077 0.42723 4
31 5KR7 6X9 0.001706 0.42288 4
32 4D4U FUC NDG GAL FUC 0.009803 0.41235 4
33 3KDJ A8S 0.01388 0.40916 4
34 5A89 ADP 0.04316 0.4091 4
35 5A89 FMN 0.04316 0.4091 4
36 1DZK PRZ 0.00425 0.40118 4
37 3RDO BTN 0.005181 0.42411 4.57516
38 5I0U DCY 0.00006021 0.51194 4.66667
39 4Y3O OGA 0.001525 0.45304 4.66667
40 4YZC STU 0.007311 0.44454 4.66667
41 2V58 LZJ 0.02394 0.42387 4.66667
42 4RPO T6C 0.01133 0.42331 4.66667
43 5EB4 FAD 0.03195 0.41533 4.66667
44 4BJ8 BTN 0.009858 0.41262 4.66667
45 4CCK OGA 0.00178 0.41151 4.66667
46 1ERB ETR 0.02065 0.41131 4.66667
47 5IXH OTP 0.01736 0.43053 5.33333
48 5X1M DHB 0.01354 0.42466 5.33333
49 3A7R LAQ 0.02168 0.41958 5.33333
50 2JLD AG1 0.01935 0.41777 5.33333
51 5FLJ QUE 0.00006637 0.52869 6
52 2XUM OGA 0.000009371 0.50517 6
53 3PQB VGP 0.0013 0.46415 6
54 4MNS 2AX 0.00543 0.46221 6
55 4HPH SUC 0.006676 0.41874 6
56 1FKB RAP 0.02207 0.4136 6.54206
57 1DRY AAG 0.0008074 0.48344 6.66667
58 1DRY AKG 0.0008074 0.48344 6.66667
59 1TT8 PHB 0.008331 0.43014 6.66667
60 1QY1 PRZ 0.006947 0.42774 6.66667
61 5DEY 59T 0.016 0.42657 6.66667
62 1BHX ASP PHE GLU GLU ILE 0.007354 0.40226 6.66667
63 4ZU5 THM 0.003135 0.43699 6.94444
64 4GJY OGA 0.00001127 0.55909 7.33333
65 1GQG DCD 0.00004103 0.54138 7.33333
66 4ZXA H8N 0.0009982 0.45066 7.33333
67 5A5W GUO 0.01673 0.42954 7.33333
68 2BOS GLA GAL 0.00563 0.40285 7.35294
69 5F3I 5UJ 0.001395 0.49862 8
70 5IVE 6E8 0.001095 0.48124 8
71 2Q8C AKG 0.0006003 0.47095 8
72 1GP6 DH2 0.001648 0.46436 8
73 1GP6 QUE 0.001776 0.46436 8
74 1GP6 SIN 0.001648 0.46436 8
75 5LY2 OGA 0.001138 0.45561 8
76 2OS2 OGA 0.001251 0.45464 8
77 2YBP 2HG 0.00138 0.45265 8
78 3RGA LSB 0.002218 0.44435 8
79 2Q8E OGA 0.000891 0.43594 8
80 2P5B OGA 0.003906 0.4277 8
81 5FWE OGA 0.0008789 0.42524 8
82 1OIJ AKG 0.001053 0.40975 8
83 3RGA ILD 0.02256 0.40512 8
84 5N87 N66 0.04024 0.40425 8
85 5ML3 DL3 0.002078 0.47448 8.05369
86 1FDQ HXA 0.01907 0.41441 8.39695
87 3WG3 A2G GAL NAG FUC 0.001169 0.43021 8.66667
88 4BXF AKG 0.005349 0.4238 8.66667
89 5EPA AKG 0.003569 0.41881 8.66667
90 4D06 NAR 0.02428 0.4004 8.66667
91 5FQ0 FLC 0.0004015 0.47888 8.77193
92 1WUB OTP 0.01848 0.42906 9.33333
93 3ZDS HMQ 0.006645 0.4141 9.33333
94 4ZU4 4TG 0.0002891 0.48759 9.45946
95 5A3T MMK 0.0004535 0.50102 10
96 5BYZ 4WE 0.007933 0.43672 10
97 5U98 1KX 0.04152 0.40827 10.101
98 4NS0 PIO 0.01293 0.40341 10.5263
99 3OPT AKG 0.0006207 0.47004 10.6667
100 4XCB HY0 0.002161 0.46002 10.6667
101 4FFG LBS 0.001841 0.4435 10.6667
102 5UQD AKG 0.003419 0.43243 10.6667
103 4XCB AKG 0.004035 0.41508 10.6667
104 4RFR RHN 0.003071 0.44165 11.3333
105 5FPX GLY SER SER HIS HIS HIS HIS HIS 0.00001174 0.4753 11.5044
106 4BQY FNT 0.00008269 0.42895 12
107 3HQR OGA 0.001786 0.42172 12
108 5L9B AKG 0.004199 0.41223 12
109 5L9V OGA 0.004283 0.41169 12
110 4QM9 CYS 0.000004056 0.58208 12.6667
111 1LRH NLA 0.00002389 0.53115 12.6667
112 3MPB FRU 0.00001422 0.49835 12.6667
113 2QZ3 XYP XYP XYP 0.01623 0.40923 12.6667
114 5JSP DQY 0.0000002709 0.58744 13.3333
115 2YNE NHW 0.01182 0.45704 13.3333
116 2YNE YNE 0.01182 0.45704 13.3333
117 4N7C AEF 0.002047 0.44866 13.3333
118 4XAC AKG 0.001764 0.42311 13.3333
119 4J25 OGA 0.0002732 0.48916 14
120 5C5T AKG 0.001628 0.44057 14
121 3FYS PLM 0.01359 0.41631 14
122 3H9A PPY 0.00008163 0.49412 15.3333
123 3AMN CBI 0.01697 0.41141 15.3333
124 3AMN CBK 0.01697 0.41141 15.3333
125 2ARC ARA 0.001426 0.44331 15.8537
126 2JIG PD2 0.0003814 0.47051 16
127 5U55 S0H 0.002911 0.44845 16
128 2FCU AKG 0.0006112 0.44289 16
129 4WW7 AMP 0.008982 0.42214 16.6667
130 5HZX 2GE 0.00317 0.41862 16.6667
131 3H7J PPY 0.00004614 0.48106 17.3333
132 4QXB OGA 0.008316 0.40687 17.3333
133 4M26 ZZU 0.002142 0.46022 18
134 4M26 SIN 0.002142 0.46022 18
135 1J3R 6PG 0.00004755 0.51684 19.3333
136 4YRD 3IT 0.000004407 0.57741 20
137 2NNQ T4B 0.04506 0.40453 20.6107
138 2GC0 PAN 0.00002561 0.47489 20.6667
139 5IQT AKG 0.0002264 0.42037 28
140 5IQT 6CU 0.0003548 0.40167 28
Pocket No.: 2; Query (leader) PDB : 5TFZ; Ligand: 7BC; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5tfz.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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