Receptor
PDB id Resolution Class Description Source Keywords
2Y91 2 Å EC: 3.5.2.6 CRYSTAL STRUCTURE OF CLASS A BETA-LACTAMASE FROM BACILLUS LICHENIFORMIS BS3 WITH CLAVULANIC ACID BACILLUS LICHENIFORMIS HYDROLASE
Ref.: NOVEL FRAGMENTS OF CLAVULANATE OBSERVED IN THE STRU THE CLASS A BETA-LACTAMASE FROM BACILLUS LICHENIFOR J.ANTIMICROB.CHEMOTHER. V. 67 2379 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
98J A:1293;
B:1293;
B:1294;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
132.115 C5 H8 O4 C(CO)...
CIT A:1294;
Invalid;
none;
submit data
192.124 C6 H8 O7 C(C(=...
PGE A:1295;
Invalid;
none;
submit data
150.173 C6 H14 O4 C(COC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2Y91 2 Å EC: 3.5.2.6 CRYSTAL STRUCTURE OF CLASS A BETA-LACTAMASE FROM BACILLUS LICHENIFORMIS BS3 WITH CLAVULANIC ACID BACILLUS LICHENIFORMIS HYDROLASE
Ref.: NOVEL FRAGMENTS OF CLAVULANATE OBSERVED IN THE STRU THE CLASS A BETA-LACTAMASE FROM BACILLUS LICHENIFOR J.ANTIMICROB.CHEMOTHER. V. 67 2379 2012
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 35 families.
1 3SOI - CIT C6 H8 O7 C(C(=O)O)C....
2 2Y91 - 98J C5 H8 O4 C(CO)C(=O)....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 29 families.
1 3SOI - CIT C6 H8 O7 C(C(=O)O)C....
2 2Y91 - 98J C5 H8 O4 C(CO)C(=O)....
3 1W7F - ICT C6 H8 O7 C([C@@H]([....
50% Homology Family (32)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 15 families.
1 5EOE - CIT C6 H8 O7 C(C(=O)O)C....
2 5EOO - CIT C6 H8 O7 C(C(=O)O)C....
3 3BFF - FPM C12 H15 N O5 S C[C@H]([C@....
4 5UJ3 - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
5 5UJ4 - SFR C12 H17 N O6 S C[C@H]([C@....
6 4QB8 - 1TE C16 H21 N3 O4 S2 C[C@@H]1[C....
7 3NY4 - SMX C18 H18 N6 O5 S2 Cn1c(nnn1)....
8 5TWE - CAZ C17 H19 N5 O7 S2 CC(C)(C(=O....
9 4XXR - JSC C22 H17 N2 O6 Ru S CC1([C@@H]....
10 3G31 Ki = 1.3 mM GF1 C12 H15 N O4 C[C@@H](C(....
11 3G34 Ki = 1.1 mM 1CE C12 H12 N6 O S C1CCc2c(c3....
12 3HLW - CE3 C16 H17 N5 O7 S2 CC(=O)OCC1....
13 3G30 Ki = 3.1 mM G30 C11 H9 F2 N O3 c1cc(c(cc1....
14 3HVF - PNK C16 H20 N2 O5 S CC1([C@@H]....
15 3G32 Ki = 0.194 mM 3G3 C11 H9 N5 O2 c1ccc2c(c1....
16 3G2Z Ki = 4.4 mM GZ2 C7 H9 N5 O C1CC(=CC(=....
17 3G35 Ki = 0.021 mM F13 C14 H10 F N5 O c1cc(cc(c1....
18 5FQJ - 6NT C6 H4 N4 O2 c1cc2c(cc1....
19 5FQK Kd = 15.8 uM 6NT C6 H4 N4 O2 c1cc2c(cc1....
20 5NE2 Ki = 84 pM DGL C5 H9 N O4 C(CC(=O)O)....
21 2ZD8 - MER C17 H27 N3 O5 S C[C@@H]1[C....
22 1VM1 - TAZ C10 H12 N4 O5 S C[C@@]1([C....
23 3MKE - CZ6 C16 H25 B N4 O6 S B1(O[C@H](....
24 4FH2 - 0RN C8 H11 N O5 S CC1([C@@H]....
25 3SOI - CIT C6 H8 O7 C(C(=O)O)C....
26 2Y91 - 98J C5 H8 O4 C(CO)C(=O)....
27 1PZP Ki = 480 uM FTA C16 H13 N7 c1ccc(cc1)....
28 1PZO Ki = 460 uM CBT C15 H13 Cl2 N5 c1cc(ccc1C....
29 1NY0 - NBF C14 H16 B N O4 B(CNC(=O)c....
30 1NXY - SM2 C14 H14 B N O5 S B([C@H](c1....
31 3P98 - CIT C6 H8 O7 C(C(=O)O)C....
32 1W7F - ICT C6 H8 O7 C([C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 98J; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 98J 1 1
2 MLA 0.428571 0.608696
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2Y91; Ligand: 98J; Similar sites found: 60
This union binding pocket(no: 1) in the query (biounit: 2y91.bio2) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4MBY BGC SIA GAL 0.01613 0.40555 1.79856
2 4YJI TYL 0.01073 0.41391 1.88679
3 5JXZ ISJ 0.02202 0.40619 1.88679
4 5JXZ ISC 0.02376 0.40619 1.88679
5 5JY4 ISC 0.02051 0.40442 1.88679
6 4KQR VPP 0.0001555 0.52164 2.26415
7 1V9N NDP 0.0403 0.41157 2.26415
8 1EQ2 NAP 0.01162 0.43453 2.64151
9 2X6T NAP 0.01256 0.43203 2.64151
10 1Y0Y L2O VAL VAL ASP 0.007037 0.4234 2.64151
11 4R6W SAH 0.0147 0.41772 2.64151
12 5GM9 CBK 0.02732 0.41757 2.8169
13 3HUN ZZ7 0.00001784 0.45685 3.01887
14 5L2J 6UL 0.02577 0.45143 3.01887
15 5L2J 70E 0.02688 0.45143 3.01887
16 1EBG PAH 0.02861 0.40965 3.01887
17 1B7H LYS NLE LYS 0.02565 0.41916 3.39623
18 3EAU PDN 0.04437 0.40742 3.39623
19 3I53 SAH 0.02889 0.40376 3.39623
20 3L8W XAN 0.04947 0.40248 3.39623
21 3UEC ALA ARG TPO LYS 0.006717 0.40821 3.42466
22 3TNF GNP 0.03708 0.40385 4.02299
23 2MBR FAD 0.03011 0.41197 4.15094
24 3E9I XAH 0.03305 0.40971 4.15094
25 5GXU FAD 0.03498 0.40156 4.5283
26 4MRT COA 0.0179 0.42614 4.74138
27 3HV8 C2E 0.006674 0.43343 4.85075
28 2IMP NAI 0.02495 0.42335 4.90566
29 1SU2 ATP 0.01522 0.41388 5.03145
30 5LYH 7B8 0.04182 0.40318 5.18135
31 1U7Z PMT 0.01504 0.42771 5.30973
32 1YQS BSA 0.0009519 0.50308 5.66038
33 1OKE BOG 0.01027 0.40995 5.66038
34 5TA6 79D 0.04005 0.40239 6.03774
35 2J3M PRI 0.01926 0.42687 6.41509
36 1P0F NAP 0.01092 0.42409 6.41509
37 2J3M ATP 0.02474 0.41937 6.41509
38 2VSU ACO 0.02013 0.40404 6.41509
39 3ZLB ANP 0.02607 0.40273 6.41509
40 1X7D NAD 0.01181 0.43079 6.79245
41 1X7D ORN 0.01861 0.42694 6.79245
42 4PYW ACE THR THR ALA ILE NH2 0.0211 0.41943 6.79245
43 4QVB F42 0.02038 0.41763 6.80272
44 3A5Z KAA 0.02562 0.40432 6.80628
45 3VEH 0GA 0.01996 0.41469 7.16981
46 4N8I COA 0.0176 0.42318 7.54717
47 4HY1 19X 0.007505 0.41397 7.54717
48 1EWY FAD 0.01816 0.41249 7.54717
49 2Z6J FMN 0.03951 0.40315 7.54717
50 5N2D 8J8 0.01084 0.42944 7.63889
51 2IL4 COA 0.01724 0.41788 7.76699
52 4K91 SIN 0.002235 0.41335 7.92453
53 2CJ9 SSA 0.007157 0.44739 8.67924
54 2WSA MYA 0.04506 0.42565 9.43396
55 2WSA 646 0.04506 0.42565 9.43396
56 4CKU P2F 0.04392 0.40315 11.3208
57 2BVE PH5 0.009058 0.41093 11.7647
58 2RKV COA 0.04581 0.40234 13.9623
59 4WXG 2BO 0.01757 0.41114 16.2264
60 4K30 NLG 0.01485 0.41452 21.875
Pocket No.: 2; Query (leader) PDB : 2Y91; Ligand: 98J; 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: 2y91.bio2) has 3 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2Y91; Ligand: 98J; Similar sites found: 14
This union binding pocket(no: 3) in the query (biounit: 2y91.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2VZZ SCA 0.03942 0.4038 1.83486
2 3T4L ZEA 0.02246 0.40292 2.26415
3 2EFX NFA 0.01198 0.41437 2.64151
4 5JJU AMP 0.02275 0.40001 2.64151
5 4H2D FMN 0.01025 0.42862 3.63636
6 2OAT PFM 0.02285 0.40773 3.77358
7 1NE7 16G 0.00812 0.41311 4.90566
8 3R96 ACO 0.04153 0.41318 5.31915
9 3R96 AMP 0.04153 0.41318 5.31915
10 3ZOD HQE 0.03689 0.40181 6.80628
11 3Q9T FAY 0.04018 0.41577 7.92453
12 2GJP BGC GLC DAF GLC GLC GLC DAF 0.03796 0.43176 9.0566
13 4ZFL 4NK 0.005031 0.44711 10.6838
14 5F2T PLM 0.02626 0.41146 13.3117
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