Receptor
PDB id Resolution Class Description Source Keywords
6D19 1.45 Å EC: 3.5.2.6 CRYSTAL STRUCTURE OF KPC-2 COMPLEXED WITH COMPOUND 9 KLEBSIELLA PNEUMONIAE BETA-LACTAMASE CARBAPENEMASE PHOSPHONATE INHIBITOR HYDROHYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: HETEROARYL PHOSPHONATES AS NONCOVALENT INHIBITORS O SERINE- AND METALLOCARBAPENEMASES. J.MED.CHEM. V. 62 8480 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:304;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
YKG A:303;
A:302;
A:301;
Valid;
Valid;
Valid;
none;
none;
none;
Ki = 0.246 uM
333.072 C11 H10 Br O5 P Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6D19 1.45 Å EC: 3.5.2.6 CRYSTAL STRUCTURE OF KPC-2 COMPLEXED WITH COMPOUND 9 KLEBSIELLA PNEUMONIAE BETA-LACTAMASE CARBAPENEMASE PHOSPHONATE INHIBITOR HYDROHYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: HETEROARYL PHOSPHONATES AS NONCOVALENT INHIBITORS O SERINE- AND METALLOCARBAPENEMASES. J.MED.CHEM. V. 62 8480 2019
Members (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 48 families.
1 6XJ8 Kd = 220 uM 8YF C12 H19 N3 O5 S [H]/N=C/NC....
2 6MEY Ki = 479 uM O5E C15 H14 N6 O c1ccc(cc1)....
3 6D15 Ki = 32.9 uM TWB C12 H13 O5 P Cc1cc2c(cc....
4 6D18 Ki = 1.4 uM GTV C12 H13 O5 P Cc1cc(c2c(....
5 6D17 Ki = 15.3 uM VKE C11 H9 O7 P c1c2c(cc3c....
6 6XD7 - ZZ7 C16 H21 N3 O5 S CC1([C@@H]....
7 6V1J - QNA C10 H9 B F O5 [B-]1([C@@....
8 6M7I Ki = 386 uM J84 C10 H7 Cl2 N7 c1cc(c(cc1....
9 5UJ3 - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
10 6D16 Ki = 8.4 uM FUJ C11 H11 O6 P COc1ccc2c(....
11 6D19 Ki = 0.246 uM YKG C11 H10 Br O5 P Cc1cc2c(c(....
12 6MLL Ki = 239 uM N1G C17 H13 N7 O c1ccc(cc1)....
13 5UJ4 - SFR C12 H17 N O6 S C[C@H]([C@....
14 6MNP - 1CE C12 H12 N6 O S C1CCc2c(c3....
70% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 41 families.
1 6XJ8 Kd = 220 uM 8YF C12 H19 N3 O5 S [H]/N=C/NC....
2 6MEY Ki = 479 uM O5E C15 H14 N6 O c1ccc(cc1)....
3 6D15 Ki = 32.9 uM TWB C12 H13 O5 P Cc1cc2c(cc....
4 6D18 Ki = 1.4 uM GTV C12 H13 O5 P Cc1cc(c2c(....
5 6D17 Ki = 15.3 uM VKE C11 H9 O7 P c1c2c(cc3c....
6 6XD7 - ZZ7 C16 H21 N3 O5 S CC1([C@@H]....
7 6V1J - QNA C10 H9 B F O5 [B-]1([C@@....
8 6M7I Ki = 386 uM J84 C10 H7 Cl2 N7 c1cc(c(cc1....
9 5UJ3 - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
10 6D16 Ki = 8.4 uM FUJ C11 H11 O6 P COc1ccc2c(....
11 6D19 Ki = 0.246 uM YKG C11 H10 Br O5 P Cc1cc2c(c(....
12 6MLL Ki = 239 uM N1G C17 H13 N7 O c1ccc(cc1)....
13 5UJ4 - SFR C12 H17 N O6 S C[C@H]([C@....
14 6MNP - 1CE C12 H12 N6 O S C1CCc2c(c3....
50% Homology Family (57)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 23 families.
1 5EOE - CIT C6 H8 O7 C(C(=O)O)C....
2 5EOO - CIT C6 H8 O7 C(C(=O)O)C....
3 6XJ8 Kd = 220 uM 8YF C12 H19 N3 O5 S [H]/N=C/NC....
4 6MEY Ki = 479 uM O5E C15 H14 N6 O c1ccc(cc1)....
5 6D15 Ki = 32.9 uM TWB C12 H13 O5 P Cc1cc2c(cc....
6 6D18 Ki = 1.4 uM GTV C12 H13 O5 P Cc1cc(c2c(....
7 6D17 Ki = 15.3 uM VKE C11 H9 O7 P c1c2c(cc3c....
8 6XD7 - ZZ7 C16 H21 N3 O5 S CC1([C@@H]....
9 6V1J - QNA C10 H9 B F O5 [B-]1([C@@....
10 6M7I Ki = 386 uM J84 C10 H7 Cl2 N7 c1cc(c(cc1....
11 5UJ3 - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
12 6D16 Ki = 8.4 uM FUJ C11 H11 O6 P COc1ccc2c(....
13 6D19 Ki = 0.246 uM YKG C11 H10 Br O5 P Cc1cc2c(c(....
14 6MLL Ki = 239 uM N1G C17 H13 N7 O c1ccc(cc1)....
15 5UJ4 - SFR C12 H17 N O6 S C[C@H]([C@....
16 6MNP - 1CE C12 H12 N6 O S C1CCc2c(c3....
17 3BFF - FPM C12 H15 N O5 S C[C@H]([C@....
18 6B68 - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
19 6B6F - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
20 6B69 - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
21 6B6A - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
22 4QB8 - 1TE C16 H21 N3 O4 S2 C[C@@H]1[C....
23 6B6C - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
24 6B6D - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
25 3NY4 - SMX C18 H18 N6 O5 S2 Cn1c(nnn1)....
26 6B6E - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
27 6CYU - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
28 5TWE - CAZ C17 H19 N5 O7 S2 CC(C)(C(=O....
29 4XXR - JSC C22 H17 N2 O6 Ru S CC1([C@@H]....
30 6MIA - 1CE C12 H12 N6 O S C1CCc2c(c3....
31 3G31 Ki = 1.3 mM GF1 C12 H15 N O4 C[C@@H](C(....
32 3G34 Ki = 1.1 mM 1CE C12 H12 N6 O S C1CCc2c(c3....
33 3HLW - CE3 C16 H17 N5 O7 S2 CC(=O)OCC1....
34 3G30 Ki = 3.1 mM G30 C11 H9 F2 N O3 c1cc(c(cc1....
35 6CYQ - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
36 3HVF - PNK C16 H20 N2 O5 S CC1([C@@H]....
37 3G32 Ki = 0.194 mM 3G3 C11 H9 N5 O2 c1ccc2c(c1....
38 3G2Z Ki = 4.4 mM GZ2 C7 H9 N5 O C1CC(=CC(=....
39 6BU3 Ki = 0.28 uM 3GK C16 H10 F3 N7 O c1cc(cc(c1....
40 3G35 Ki = 0.021 mM F13 C14 H10 F N5 O c1cc(cc(c1....
41 5FQJ - 6NT C6 H4 N4 O2 c1cc2c(cc1....
42 6TY6 - 6NT C6 H4 N4 O2 c1cc2c(cc1....
43 5FQK Kd = 15.8 uM 6NT C6 H4 N4 O2 c1cc2c(cc1....
44 5NE2 Ki = 84 pM DGL C5 H9 N O4 C(CC(=O)O)....
45 6QW7 - DSN C3 H7 N O3 C([C@H](C(....
46 2ZD8 - MER C17 H27 N3 O5 S C[C@@H]1[C....
47 1VM1 - TAZ C10 H12 N4 O5 S C[C@@]1([C....
48 3MKE - CZ6 C16 H25 B N4 O6 S B1(O[C@H](....
49 4FH2 - 0RN C8 H11 N O5 S CC1([C@@H]....
50 3SOI - CIT C6 H8 O7 C(C(=O)O)C....
51 2Y91 - 98J C5 H8 O4 C(CO)C(=O)....
52 1PZP Ki = 480 uM FTA C16 H13 N7 c1ccc(cc1)....
53 1PZO Ki = 460 uM CBT C15 H13 Cl2 N5 c1cc(ccc1C....
54 1NY0 - NBF C14 H16 B N O4 B(CNC(=O)c....
55 1NXY - SM2 C14 H14 B N O5 S B([C@H](c1....
56 3P98 - CIT C6 H8 O7 C(C(=O)O)C....
57 1W7F - ICT C6 H8 O7 C([C@@H]([....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: YKG; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 YKG 1 1
2 GTV 0.62069 0.877551
3 XJE 0.590164 0.826923
4 P9T 0.492063 0.9375
5 TWB 0.421875 0.877551
Similar Ligands (3D)
Ligand no: 1; Ligand: YKG; Similar ligands found: 134
No: Ligand Similarity coefficient
1 7SX 0.9900
2 L8J 0.9703
3 FUJ 0.9615
4 KED 0.9352
5 F95 0.9349
6 CX4 0.9268
7 VKE 0.9256
8 M3Q 0.9224
9 T6Z 0.9185
10 QMS 0.9185
11 EY7 0.9139
12 GSY 0.9137
13 9LI 0.9131
14 CLI 0.9122
15 I59 0.9078
16 790 0.9066
17 IBM 0.9053
18 8RK 0.9038
19 TRF 0.9014
20 H05 0.9012
21 LZB 0.9009
22 X04 0.8996
23 JHY 0.8996
24 EV3 0.8995
25 9UG 0.8991
26 GO0 0.8991
27 EYA 0.8984
28 JYT 0.8968
29 EYM 0.8937
30 ST1 0.8934
31 XM5 0.8932
32 PMP 0.8909
33 7M2 0.8906
34 NLA 0.8905
35 PLP 0.8903
36 MS0 0.8902
37 AVR 0.8892
38 NPL 0.8890
39 PXP 0.8886
40 AO6 0.8885
41 KWQ 0.8858
42 IOS 0.8855
43 JYW 0.8855
44 JXK 0.8845
45 JY2 0.8845
46 FXH 0.8844
47 K68 0.8844
48 96R 0.8841
49 GNR 0.8830
50 7FF 0.8827
51 JYK 0.8817
52 CSN 0.8814
53 ALN 0.8813
54 EXL 0.8806
55 CRZ 0.8801
56 B61 0.8797
57 6DP 0.8793
58 JXT 0.8793
59 HHT 0.8784
60 9F8 0.8780
61 TXW 0.8779
62 982 0.8779
63 5OF 0.8773
64 FWB 0.8772
65 JXZ 0.8758
66 C8O 0.8757
67 8GK 0.8753
68 96U 0.8749
69 3N4 0.8736
70 LP8 0.8732
71 67X 0.8726
72 AJD 0.8717
73 AKD 0.8711
74 2J9 0.8704
75 Q9P 0.8703
76 96Z 0.8702
77 8Y7 0.8701
78 SG6 0.8701
79 8HG 0.8701
80 KWH 0.8699
81 MAG 0.8698
82 E7R 0.8693
83 0J5 0.8687
84 W8G 0.8681
85 39Z 0.8677
86 7M6 0.8674
87 5PX 0.8671
88 JXW 0.8667
89 9FQ 0.8664
90 JR2 0.8664
91 LOG 0.8661
92 A0O 0.8661
93 XFE 0.8658
94 JUO 0.8656
95 KZ9 0.8656
96 2J2 0.8653
97 MW5 0.8651
98 BA5 0.8651
99 PYU 0.8649
100 9KZ 0.8645
101 RH1 0.8643
102 IOP 0.8643
103 L07 0.8638
104 W22 0.8636
105 TQU 0.8635
106 IAC 0.8631
107 BK9 0.8629
108 SBK 0.8629
109 N88 0.8628
110 TRP 0.8625
111 657 0.8620
112 TSR 0.8619
113 MQG 0.8617
114 G6P 0.8612
115 5WU 0.8611
116 5NS 0.8611
117 EXR 0.8603
118 SNG 0.8602
119 GC2 0.8601
120 EPR 0.8600
121 NAG 0.8599
122 K66 0.8593
123 57O 0.8592
124 GO1 0.8591
125 O83 0.8590
126 XG1 0.8586
127 LZ2 0.8585
128 2LB 0.8585
129 4OG 0.8583
130 MQB 0.8579
131 30G 0.8557
132 S0I 0.8552
133 8DA 0.8550
134 ST4 0.8548
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6D19; Ligand: YKG; 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: 6d19.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6D19; Ligand: YKG; 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: 6d19.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 6D19; Ligand: YKG; 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: 6d19.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
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