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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 38 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 32 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 (42)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 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 6B68 - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
7 6B6F - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
8 6B69 - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
9 6B6A - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
10 4QB8 - 1TE C16 H21 N3 O4 S2 C[C@@H]1[C....
11 6B6C - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
12 6B6D - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
13 3NY4 - SMX C18 H18 N6 O5 S2 Cn1c(nnn1)....
14 6B6E - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
15 6CYU - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
16 5TWE - CAZ C17 H19 N5 O7 S2 CC(C)(C(=O....
17 4XXR - JSC C22 H17 N2 O6 Ru S CC1([C@@H]....
18 3G31 Ki = 1.3 mM GF1 C12 H15 N O4 C[C@@H](C(....
19 3G34 Ki = 1.1 mM 1CE C12 H12 N6 O S C1CCc2c(c3....
20 3HLW - CE3 C16 H17 N5 O7 S2 CC(=O)OCC1....
21 3G30 Ki = 3.1 mM G30 C11 H9 F2 N O3 c1cc(c(cc1....
22 6CYQ - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
23 3HVF - PNK C16 H20 N2 O5 S CC1([C@@H]....
24 3G32 Ki = 0.194 mM 3G3 C11 H9 N5 O2 c1ccc2c(c1....
25 3G2Z Ki = 4.4 mM GZ2 C7 H9 N5 O C1CC(=CC(=....
26 6BU3 Ki = 0.28 uM 3GK C16 H10 F3 N7 O c1cc(cc(c1....
27 3G35 Ki = 0.021 mM F13 C14 H10 F N5 O c1cc(cc(c1....
28 5FQJ - 6NT C6 H4 N4 O2 c1cc2c(cc1....
29 5FQK Kd = 15.8 uM 6NT C6 H4 N4 O2 c1cc2c(cc1....
30 5NE2 Ki = 84 pM DGL C5 H9 N O4 C(CC(=O)O)....
31 2ZD8 - MER C17 H27 N3 O5 S C[C@@H]1[C....
32 1VM1 - TAZ C10 H12 N4 O5 S C[C@@]1([C....
33 3MKE - CZ6 C16 H25 B N4 O6 S B1(O[C@H](....
34 4FH2 - 0RN C8 H11 N O5 S CC1([C@@H]....
35 3SOI - CIT C6 H8 O7 C(C(=O)O)C....
36 2Y91 - 98J C5 H8 O4 C(CO)C(=O)....
37 1PZP Ki = 480 uM FTA C16 H13 N7 c1ccc(cc1)....
38 1PZO Ki = 460 uM CBT C15 H13 Cl2 N5 c1cc(ccc1C....
39 1NY0 - NBF C14 H16 B N O4 B(CNC(=O)c....
40 1NXY - SM2 C14 H14 B N O5 S B([C@H](c1....
41 3P98 - CIT C6 H8 O7 C(C(=O)O)C....
42 1W7F - ICT C6 H8 O7 C([C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 98J; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 98J 1 1
2 3OH 0.571429 0.695652
3 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 with APoc: 97
This union binding pocket(no: 1) in the query (biounit: 2y91.bio2) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 4MBY BGC SIA GAL 1.79856
2 4YJI TYL 1.88679
3 5JXZ ISC 1.88679
4 5JXZ ISJ 1.88679
5 5JY4 ISC 1.88679
6 4PXL NAD 1.88679
7 4FOJ C2E 1.89394
8 4KQR VPP 2.26415
9 2ZTG A5A 2.26415
10 6DWD GTP 2.26415
11 6DWD HDV 2.26415
12 1V9N NDP 2.26415
13 3T4L ZEA 2.26415
14 2X6T NAP 2.64151
15 1Y0Y L2O VAL VAL ASP 2.64151
16 1EQ2 NAP 2.64151
17 4R6W SAH 2.64151
18 2ZBA COA 2.64151
19 2QE0 NAP 2.64151
20 5GM9 CBK 2.8169
21 3HUN ZZ7 3.01887
22 5WL1 D3D 3.01887
23 5WL1 CUY 3.01887
24 1EBG PAH 3.01887
25 5MRH Q9Z 3.3046
26 5VKM GAL SIA 3.39623
27 1B7H LYS NLE LYS 3.39623
28 3EAU NDP 3.39623
29 3EAU PDN 3.39623
30 3I53 SAH 3.39623
31 3L8W XAN 3.39623
32 3UEC ALA ARG TPO LYS 3.42466
33 2OAT PFM 3.77358
34 5GVH FMN 3.77358
35 1YNQ NDP 3.77358
36 6F97 FAD 3.77358
37 3TNF GNP 4.02299
38 3N3T C2E 4.15094
39 5O7E 9NB 4.15094
40 2MBR FAD 4.15094
41 3E9I XAH 4.15094
42 1PL6 NAD 4.15094
43 5FI3 NAP 4.15094
44 3OFK SAH 4.16667
45 5OJ7 AR6 4.5283
46 5XVG 8FX 4.5283
47 6BKA FMN 4.5283
48 5GXU FAD 4.5283
49 4MRT COA 4.74138
50 1QR0 COA 4.82456
51 3HV8 C2E 4.85075
52 2IMP NAI 4.90566
53 5M1T C2E 4.90566
54 1SU2 ATP 5.03145
55 1U7Z PMT 5.30973
56 1YQS BSA 5.66038
57 6DQU GLY ILE ILE ASN THR LEU 5.66038
58 1OKE BOG 5.66038
59 5V59 8X1 6.03774
60 5TA6 79D 6.03774
61 1G8K MGD 6.03774
62 3TCT 3MI 6.29921
63 2J3M PRI 6.41509
64 1P0F NAP 6.41509
65 2J3M ATP 6.41509
66 5O0B 9FE 6.41509
67 2VSU ACO 6.41509
68 3ZLB ANP 6.41509
69 1X7D NAD 6.79245
70 1X7D ORN 6.79245
71 4PYW ACE THR THR ALA ILE NH2 6.79245
72 4QVB F42 6.80272
73 3A5Z KAA 6.80628
74 3VEH 0GA 7.16981
75 4N8I COA 7.54717
76 4HY1 19X 7.54717
77 1EWY FAD 7.54717
78 2Z6J FMN 7.54717
79 5N2D 8J8 7.63889
80 5LXT GTP 7.69231
81 2IL4 COA 7.76699
82 4K91 SIN 7.92453
83 4I42 1HA 8.30189
84 2CJ9 SSA 8.67924
85 5OC1 FAD 9.0566
86 2WSA 646 9.43396
87 2WSA MYA 9.43396
88 1KRR ACO 9.85222
89 2BVE PH5 11.7647
90 5Z99 SLB 12.0755
91 5NWD 9C8 12.2449
92 4UOX PUT 13.2075
93 2RKV COA 13.9623
94 4WXG 2BO 16.2264
95 4FOU C2E 16.2393
96 6B2M COA 21.5094
97 4K30 NLG 21.875
Pocket No.: 2; Query (leader) PDB : 2Y91; Ligand: 98J; 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: 2y91.bio2) has 3 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2Y91; Ligand: 98J; Similar sites found with APoc: 22
This union binding pocket(no: 3) in the query (biounit: 2y91.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 2VZZ SCA 1.83486
2 2EFX NFA 2.64151
3 5JJU AMP 2.64151
4 5D2R 56W 3.39623
5 4JTA NAP 3.39623
6 4H2D FMN 3.63636
7 1B1C FMN 4.41989
8 2ZA5 2FF 4.5283
9 1NE7 16G 4.90566
10 3DST GRG 5.28302
11 3R96 ACO 5.31915
12 3R96 AMP 5.31915
13 1RM0 NAI 5.66038
14 3ZOD HQE 6.80628
15 3ZOD FMN 6.80628
16 5TCI 79V 6.88406
17 5F1R 42O 7.16981
18 3Q9T FAY 7.92453
19 1XF1 CIT 9.0566
20 4ZFL 4NK 10.6838
21 5F2T PLM 13.3117
22 3KH5 AMP 15.4717
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