Receptor
PDB id Resolution Class Description Source Keywords
4RLF 1.73 Å EC: 6.-.-.- CRYSTAL STRUCTURE OF A BENZOATE COENZYME A LIGASE WITH P-TOL AND O-TOLUIC ACID RHODOPSEUDOMONAS PALUSTRIS SUBSTRATE SPECIFICITY KINETICS LIGASE
Ref.: KINETICALLY AND CRYSTALLOGRAPHICALLY GUIDED MUTATIO BENZOATE COA LIGASE (BADA) ELUCIDATE MECHANISM AND SUBSTRATE PERMISSIVITY. BIOCHEMISTRY V. 54 6230 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL B:1002;
B:1003;
B:1006;
B:1005;
A:1002;
B:1007;
B:1004;
A:1003;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
4MA A:1001;
B:1001;
Valid;
Valid;
none;
none;
submit data
136.148 C8 H8 O2 Cc1cc...
3SK A:1000;
B:1000;
Valid;
Valid;
none;
none;
submit data
136.148 C8 H8 O2 Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4RLQ 1.63 Å EC: 6.-.-.- CRYSTAL STRUCTURE OF A BENZOATE COENZYME A LIGASE WITH O-TOL RHODOPSEUDOMONAS PALUSTRIS SUBSTRATE SPECIFICITY KINETICS LIGASE
Ref.: KINETICALLY AND CRYSTALLOGRAPHICALLY GUIDED MUTATIO BENZOATE COA LIGASE (BADA) ELUCIDATE MECHANISM AND SUBSTRATE PERMISSIVITY. BIOCHEMISTRY V. 54 6230 2015
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 4RLQ - 3SK C8 H8 O2 Cc1ccccc1C....
2 4RM2 - 3U4 C7 H5 F O2 c1ccc(c(c1....
3 4RMN - C21 C5 H4 O2 S c1cc(sc1)C....
4 4RM3 - FOA C5 H4 O3 c1cc(oc1)C....
5 4RLF - 4MA C8 H8 O2 Cc1ccc(cc1....
6 4ZJZ - OOB C17 H18 N5 O8 P c1ccc(cc1)....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 4RLQ - 3SK C8 H8 O2 Cc1ccccc1C....
2 4RM2 - 3U4 C7 H5 F O2 c1ccc(c(c1....
3 4RMN - C21 C5 H4 O2 S c1cc(sc1)C....
4 4RM3 - FOA C5 H4 O3 c1cc(oc1)C....
5 4RLF - 4MA C8 H8 O2 Cc1ccc(cc1....
6 4ZJZ - OOB C17 H18 N5 O8 P c1ccc(cc1)....
7 2V7B - BEZ C7 H6 O2 c1ccc(cc1)....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 4RLQ - 3SK C8 H8 O2 Cc1ccccc1C....
2 4RM2 - 3U4 C7 H5 F O2 c1ccc(c(c1....
3 4RMN - C21 C5 H4 O2 S c1cc(sc1)C....
4 4RM3 - FOA C5 H4 O3 c1cc(oc1)C....
5 4RLF - 4MA C8 H8 O2 Cc1ccc(cc1....
6 4ZJZ - OOB C17 H18 N5 O8 P c1ccc(cc1)....
7 2V7B - BEZ C7 H6 O2 c1ccc(cc1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 4MA; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 4MA 1 1
2 ANN 0.483871 0.611111
3 1Y6 0.466667 0.625
4 Z82 0.466667 0.625
5 MBO 0.466667 0.714286
6 174 0.466667 0.625
7 BEZ 0.413793 0.909091
Ligand no: 2; Ligand: 3SK; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 3SK 1 1
2 PHT 0.555556 0.705882
3 3U4 0.454545 0.666667
4 JKE 0.454545 0.6
5 7WV 0.454545 0.666667
6 3GQ 0.451613 0.705882
7 5NE 0.447368 0.647059
8 9TZ 0.416667 0.722222
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4RLQ; Ligand: 3SK; Similar sites found: 36
This union binding pocket(no: 1) in the query (biounit: 4rlq.bio1) has 41 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2X1L MET 0.0286 0.42006 1.34875
2 2Y4O DLL 0.000002274 0.44535 4.06321
3 5MST FUM 0.000005955 0.43364 4.23892
4 5MST AMP 0.000002019 0.42446 4.23892
5 2Y4N DLL 0.00006656 0.41842 25.4005
6 4OXI GAP 0.0000001678 0.46211 28.5164
7 5MSD BEZ 0.000001409 0.43193 29.6724
8 5MSD AMP 0.000002847 0.40799 29.6724
9 5C5H 4YB 0.0000006421 0.46616 32.4503
10 5HM3 649 0.0003107 0.40072 36.9942
11 5N9X 8QN 0.0000003809 0.45537 37.7649
12 5N9X ATP 0.00000127 0.43688 37.7649
13 4GR5 APC 0.000002897 0.41756 39.1137
14 1AMU AMP 0.0000001609 0.43588 39.3064
15 3DHV DAL AMP 0.0000006411 0.45032 39.8438
16 4R0M FA5 0.000007137 0.44063 39.8844
17 4FUT ATP 0.00001151 0.40134 40.7555
18 3IES M24 0.000001069 0.48735 40.8478
19 3O84 HTJ 0.000005074 0.43575 40.8478
20 1MDB AMP DBH 0.0000006514 0.43709 41.0405
21 3KXW 1ZZ 0.0000297 0.42077 41.0405
22 4GXQ ATP 0.000004304 0.41703 41.3043
23 2D1S SLU 0.00000005118 0.51219 41.6185
24 5IE3 OXD 0.000001565 0.4644 41.6342
25 5IE3 AMP 0.000001565 0.4644 41.6342
26 4D57 ARG AMP 0.0000003957 0.50754 42.0039
27 1V25 ANP 0.0000003083 0.50563 42.9672
28 5BSR COA 0.00000044 0.54077 44.1233
29 5BSR AMP 0.000003514 0.49279 44.1233
30 3CW9 AMP 0.000000277 0.44031 44.246
31 3CW9 01A 0.0001159 0.40668 44.246
32 1PG4 PRX 0.00000008246 0.55285 45.4721
33 1PG4 COA 0.00000008246 0.55285 45.4721
34 5X8G S0N 0.0000001537 0.54926 47.0103
35 3C5E ATP 0.0000004393 0.53719 47.7842
36 5OE4 3UK 0.00000000002035 0.55227 49.14
Pocket No.: 2; Query (leader) PDB : 4RLQ; Ligand: 3SK; Similar sites found: 74
This union binding pocket(no: 2) in the query (biounit: 4rlq.bio2) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1TU3 GNP 0.03704 0.40206 None
2 4Q4K FMN 0.005115 0.44601 1.40056
3 2ZKJ ADP 0.03328 0.41653 1.52284
4 1U2Z SAH 0.03091 0.40213 1.84758
5 2GVC FAD 0.04913 0.40232 2.01342
6 3G5S FAD 0.04769 0.40695 2.0316
7 5UQW GDP 0.0272 0.40505 2.1164
8 2I0K FAD 0.04867 0.40455 2.11946
9 1XG5 NAP 0.02401 0.41702 2.15054
10 1TKE SER 0.01817 0.40764 2.23214
11 5MZY 8EZ 0.03622 0.40384 2.41935
12 4B0T ADP 0.02788 0.40592 2.43408
13 4HKP 16B 0.02469 0.40082 2.5641
14 4HKP TKW 0.03073 0.40078 2.5641
15 4RQU NAD 0.01991 0.41898 2.66667
16 3AFN NAP 0.03308 0.4117 2.71318
17 4NBU NAI 0.04074 0.40461 2.8
18 1EK0 GNP 0.03489 0.40078 2.94118
19 3R75 PYR 0.000831 0.42192 3.08285
20 2JAH NDP 0.0334 0.40928 3.23887
21 4NCN GTP 0.01697 0.41422 3.28228
22 5LRT ADP 0.02929 0.40479 3.34646
23 1XSE NDP 0.02751 0.42292 3.38983
24 5TUK FAD 0.03801 0.40272 3.43137
25 4TMZ GSP 0.01974 0.41081 3.46821
26 4K81 GTP 0.02925 0.40753 3.50877
27 2Q2V NAD 0.04257 0.40573 3.52941
28 3VEH 0GA 0.03283 0.41777 3.54767
29 1NVU GTP 0.03008 0.40555 3.61446
30 2C42 PYR 0.01171 0.43252 3.66089
31 2C42 TPP 0.01171 0.43252 3.66089
32 2F1K NAP 0.02842 0.40819 3.94265
33 3OZ2 FAD 0.04311 0.41207 4.03023
34 2JAP NDP 0.03743 0.40661 4.04858
35 1N5D NDP 0.03269 0.40979 4.16667
36 3OID NDP 0.02244 0.42085 4.26357
37 1T9D FAD 0.02653 0.42379 4.4316
38 4RJK TPP 0.01739 0.42083 4.4316
39 2E5V FAD 0.0497 0.41267 4.44915
40 1QZR ANP 0.02457 0.4102 4.54545
41 3C56 PH4 0.0235 0.40365 4.56026
42 1OX5 1PR 0.0266 0.411 4.81696
43 4XOI GTP 0.03323 0.40048 5
44 2IHT TPP 0.03743 0.40051 5.00963
45 1UPA TPP 0.03816 0.40007 5.00963
46 4RVU NDP 0.04281 0.40662 5.12048
47 3A0T ADP 0.01374 0.41386 5.26316
48 1W0J ADP BEF 0.01809 0.4095 5.29412
49 5AE2 FYC 0.04317 0.43 5.58767
50 5AE2 FAD 0.04317 0.43 5.58767
51 1CXZ GSP 0.01266 0.41919 5.81395
52 2FFQ GSP 0.03635 0.40119 5.84795
53 5IRR GSP 0.02151 0.40728 6.16883
54 5O2T GSP 0.03706 0.40074 6.41711
55 2W2X GSP 0.01781 0.40984 6.45161
56 2HF9 GSP 0.02287 0.41045 6.63717
57 3H0L ADP 0.006811 0.41589 7.44681
58 4KVG GTP 0.0346 0.40097 8.07692
59 2Z6J FMN 0.0345 0.40619 8.43373
60 5T79 NDP 0.02252 0.41486 9.33735
61 5B48 TDN 0.02017 0.41991 10.1639
62 5UFQ GNP 0.0288 0.4007 11.4754
63 1E6E FAD 0.04829 0.40571 11.7188
64 2UZI GTP 0.03005 0.40421 12.2807
65 4D0G GTP 0.01859 0.41057 13.1429
66 2CK3 ADP 0.02139 0.409 14
67 2CK3 ANP 0.02319 0.40221 14
68 1DQX BMP 0.01695 0.41264 14.9813
69 2C5L GTP 0.02365 0.41108 16.2393
70 3OII SAH 0.02271 0.40441 17.3913
71 4HIA FMN 0.02352 0.42082 21.0227
72 4DG8 AMP 0.006748 0.42559 29.8651
73 5EY9 5SV 0.004148 0.45077 37.9576
74 3E7W AMP 0.005637 0.42732 42.8571
Feedback