Receptor
PDB id Resolution Class Description Source Keywords
6D17 1.45 Å EC: 3.5.2.6 CRYSTAL STRUCTURE OF KPC-2 COMPLEXED WITH COMPOUND 3 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
VKE A:301;
 Valid;
 none;
 Ki = 15.3 uM
284.159 C11 H9 O7 P c1c2c...
GOL A:302;
 Invalid;
 none;
 submit data
92.094 C3 H8 O3 C(C(C...
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: VKE; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 VKE 1 1
2 TWB 0.551724 0.792453
3 FUJ 0.46875 0.830189
Similar Ligands (3D)
Ligand no: 1; Ligand: VKE; Similar ligands found: 125
No: Ligand Similarity coefficient
1 AO6 0.9368
2 2T4 0.9340
3 P9T 0.9292
4 YKG 0.9256
5 GTV 0.9245
6 F95 0.9230
7 EY7 0.9206
8 H05 0.9155
9 7SX 0.9148
10 3E2 0.9141
11 GNJ 0.9134
12 772 0.9129
13 CLI 0.9129
14 761 0.9077
15 A0O 0.9066
16 KM2 0.9065
17 KWQ 0.9064
18 982 0.9052
19 BN1 0.9015
20 LF5 0.9014
21 L8J 0.9002
22 AVR 0.8984
23 JT2 0.8981
24 TDH 0.8981
25 KED 0.8980
26 8RK 0.8973
27 WUB 0.8968
28 P9I 0.8968
29 GNR 0.8965
30 3N4 0.8960
31 KWH 0.8955
32 EYA 0.8953
33 ZO9 0.8953
34 MYI 0.8943
35 7ZC 0.8919
36 UMP 0.8917
37 DU 0.8917
38 GNV 0.8912
39 JHY 0.8904
40 HKK 0.8902
41 6JJ 0.8901
42 GO1 0.8894
43 9KQ 0.8893
44 8HH 0.8889
45 A04 0.8883
46 DCM 0.8878
47 EYM 0.8873
48 CRZ 0.8868
49 1YE 0.8866
50 36I 0.8855
51 CSN 0.8853
52 T6Z 0.8852
53 OAI 0.8843
54 7M2 0.8833
55 QVK 0.8830
56 PZB 0.8825
57 39Z 0.8825
58 57Q 0.8821
59 XM5 0.8814
60 0SX 0.8809
61 34L 0.8804
62 GNT 0.8795
63 XJE 0.8788
64 8G6 0.8783
65 C8O 0.8781
66 EV3 0.8778
67 9UG 0.8778
68 K75 0.8769
69 7G5 0.8768
70 LQG 0.8760
71 TXW 0.8757
72 M3Q 0.8756
73 O83 0.8746
74 JTF 0.8740
75 LJW 0.8736
76 C 0.8735
77 U5P 0.8724
78 K6N 0.8719
79 5V5 0.8716
80 AH3 0.8707
81 CX4 0.8704
82 2J2 0.8696
83 WFY 0.8695
84 V2Z 0.8688
85 TMP 0.8688
86 P1T 0.8688
87 W22 0.8687
88 XG1 0.8685
89 9L3 0.8685
90 L07 0.8681
91 FX5 0.8680
92 GO0 0.8680
93 22T 0.8677
94 I46 0.8660
95 ITP 0.8657
96 AIR 0.8653
97 YM6 0.8650
98 FBR 0.8645
99 N88 0.8644
100 IRG 0.8641
101 5KN 0.8633
102 29B 0.8632
103 0Q2 0.8625
104 7FF 0.8624
105 3RH 0.8622
106 HC8 0.8619
107 FXH 0.8617
108 90J 0.8607
109 1CE 0.8605
110 MS0 0.8605
111 NWD 0.8597
112 1M1 0.8590
113 7M5 0.8590
114 I59 0.8589
115 1TM 0.8587
116 LEB 0.8586
117 2LW 0.8584
118 77X 0.8582
119 LP8 0.8575
120 ST6 0.8570
121 KTK 0.8561
122 UNM 0.8555
123 0JO 0.8554
124 UI2 0.8553
125 D87 0.8535
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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