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Receptor
PDB id Resolution Class Description Source Keywords
5U3B 2 Å EC: 3.5.1.- PSEUDOMONAS AERUGINOSA LPXC IN COMPLEX WITH NVS-LPXC-01 PSEUDOMONAS AERUGINOSA (STRAIN ATCC 1522644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 /ORGANISM_TAXID: 208964 LPXC HYDROXYMATE GRAM NEGATIVE HYDROLASE
Ref.: DESIGN, SYNTHESIS, AND PROPERTIES OF A POTENT INHIB PSEUDOMONAS AERUGINOSA DEACETYLASE LPXC. J. MED. CHEM. V. 60 5002 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
7TD A:502;
B:502;
Valid;
Valid;
none;
none;
ic50 = 1.5 nM
319.356 C16 H21 N3 O4 CC#CC...
EPE B:503;
A:503;
Invalid;
Invalid;
none;
none;
submit data
238.305 C8 H18 N2 O4 S C1CN(...
ZN A:501;
B:501;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5U3B 2 Å EC: 3.5.1.- PSEUDOMONAS AERUGINOSA LPXC IN COMPLEX WITH NVS-LPXC-01 PSEUDOMONAS AERUGINOSA (STRAIN ATCC 1522644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 /ORGANISM_TAXID: 208964 LPXC HYDROXYMATE GRAM NEGATIVE HYDROLASE
Ref.: DESIGN, SYNTHESIS, AND PROPERTIES OF A POTENT INHIB PSEUDOMONAS AERUGINOSA DEACETYLASE LPXC. J. MED. CHEM. V. 60 5002 2017
Members (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 3UHM ic50 = 3.6 nM RFN C17 H20 N2 O5 S C[C@@](CCN....
2 4LCH - 1WN C27 H23 N3 O5 C[C@](c1cc....
3 5U3B ic50 = 1.5 nM 7TD C16 H21 N3 O4 CC#CCOc1cc....
4 4J3D ic50 = 4.4 nM 1JS C23 H25 N3 O5 c1ccc(cc1)....
5 2VES - GVR C23 H20 N2 O4 S c1ccc2cc(c....
6 5DRR - 5EN C22 H19 F2 N3 O4 C[C@]([C@@....
7 4LCG - 1WM C26 H21 N3 O5 c1cc(ccc1C....
8 3P3E - 3P3 C21 H18 N2 O4 C[C@H]([C@....
9 5N8C - 8Q8 C27 H31 N5 O3 CC(C)([C@@....
10 5DRQ - 5EM C22 H22 N4 O3 CC(C)([C@@....
11 5U39 - C90 C24 H27 N3 O5 C[C@H]([C@....
12 3U1Y ic50 = 2.13 nM 03I C25 H34 N2 O6 S C[C@@](CCc....
13 4LCF - 1WL C23 H19 N5 O3 c1cc(ccc1C....
70% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 28 families.
1 3UHM ic50 = 3.6 nM RFN C17 H20 N2 O5 S C[C@@](CCN....
2 4LCH - 1WN C27 H23 N3 O5 C[C@](c1cc....
3 5U3B ic50 = 1.5 nM 7TD C16 H21 N3 O4 CC#CCOc1cc....
4 4J3D ic50 = 4.4 nM 1JS C23 H25 N3 O5 c1ccc(cc1)....
5 2VES - GVR C23 H20 N2 O4 S c1ccc2cc(c....
6 5DRR - 5EN C22 H19 F2 N3 O4 C[C@]([C@@....
7 4LCG - 1WM C26 H21 N3 O5 c1cc(ccc1C....
8 3P3E - 3P3 C21 H18 N2 O4 C[C@H]([C@....
9 5N8C - 8Q8 C27 H31 N5 O3 CC(C)([C@@....
10 5DRQ - 5EM C22 H22 N4 O3 CC(C)([C@@....
11 5U39 - C90 C24 H27 N3 O5 C[C@H]([C@....
12 3U1Y ic50 = 2.13 nM 03I C25 H34 N2 O6 S C[C@@](CCc....
13 4LCF - 1WL C23 H19 N5 O3 c1cc(ccc1C....
14 3NZK Ki = 0.54 nM C90 C24 H27 N3 O5 C[C@H]([C@....
15 3P3G Ki = 0.18 nM 3P3 C21 H18 N2 O4 C[C@H]([C@....
16 3PS2 - UKW C13 H12 N2 O4 C[C@H]([C@....
17 3PS3 - L53 C21 H17 N3 O4 C[C@@H]([C....
18 4MQY - UKW C13 H12 N2 O4 C[C@H]([C@....
19 4IS9 - LTF C15 H20 N2 O5 CCCc1cc(cc....
20 3PS1 - UKW C13 H12 N2 O4 C[C@H]([C@....
21 4ISA - GVR C23 H20 N2 O4 S c1ccc2cc(c....
50% Homology Family (31)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 3UHM ic50 = 3.6 nM RFN C17 H20 N2 O5 S C[C@@](CCN....
2 4LCH - 1WN C27 H23 N3 O5 C[C@](c1cc....
3 5U3B ic50 = 1.5 nM 7TD C16 H21 N3 O4 CC#CCOc1cc....
4 4J3D ic50 = 4.4 nM 1JS C23 H25 N3 O5 c1ccc(cc1)....
5 2VES - GVR C23 H20 N2 O4 S c1ccc2cc(c....
6 5DRR - 5EN C22 H19 F2 N3 O4 C[C@]([C@@....
7 4LCG - 1WM C26 H21 N3 O5 c1cc(ccc1C....
8 3P3E - 3P3 C21 H18 N2 O4 C[C@H]([C@....
9 5N8C - 8Q8 C27 H31 N5 O3 CC(C)([C@@....
10 5DRQ - 5EM C22 H22 N4 O3 CC(C)([C@@....
11 5U39 - C90 C24 H27 N3 O5 C[C@H]([C@....
12 3U1Y ic50 = 2.13 nM 03I C25 H34 N2 O6 S C[C@@](CCc....
13 4LCF - 1WL C23 H19 N5 O3 c1cc(ccc1C....
14 5DRP - 5EP C23 H23 N3 O3 CC[C@H](C)....
15 4U3D - 3BX C26 H30 N2 O5 c1cc(ccc1C....
16 5U86 - 81V C25 H27 F2 N3 O5 C[C@]([C@@....
17 4U3B - 3BW C19 H20 Cl N O4 S c1cc(ccc1O....
18 5DRO - ZH2 C21 H19 N3 O4 C[C@H]([C@....
19 2J65 - MYR C14 H28 O2 CCCCCCCCCC....
20 3P3C - 3P3 C21 H18 N2 O4 C[C@H]([C@....
21 1P42 - MYR C14 H28 O2 CCCCCCCCCC....
22 3P76 - P76 C24 H27 N3 O4 C[C@H]([C@....
23 2O3Z Kd = 2 uM AI7 C14 H20 O3 CCCCCCCOc1....
24 3NZK Ki = 0.54 nM C90 C24 H27 N3 O5 C[C@H]([C@....
25 3P3G Ki = 0.18 nM 3P3 C21 H18 N2 O4 C[C@H]([C@....
26 3PS2 - UKW C13 H12 N2 O4 C[C@H]([C@....
27 3PS3 - L53 C21 H17 N3 O4 C[C@@H]([C....
28 4MQY - UKW C13 H12 N2 O4 C[C@H]([C@....
29 4IS9 - LTF C15 H20 N2 O5 CCCc1cc(cc....
30 3PS1 - UKW C13 H12 N2 O4 C[C@H]([C@....
31 4ISA - GVR C23 H20 N2 O4 S c1ccc2cc(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 7TD; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 7TD 1 1
2 5EM 0.528571 0.77193
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5U3B; Ligand: 7TD; Similar sites found with APoc: 177
This union binding pocket(no: 1) in the query (biounit: 5u3b.bio2) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 3KPE TM3 None
2 1M2Z BOG None
3 4WG0 CHD None
4 2CB8 MYA None
5 5YRL GLC GLC None
6 5HWK BEZ None
7 2ALG DAO None
8 3KO0 TFP None
9 1PTR PRB None
10 5X3R 7Y3 0.97561
11 5YJS SAL 1.67224
12 4GYS MLI 1.67224
13 1YXM ADE 1.67224
14 3ZJX BOG 1.7301
15 2BTM PGA 1.98413
16 3KP6 SAL 1.98676
17 1MJT ITU 2.00669
18 3X27 TRP 2.00669
19 4WCX ALA 2.00669
20 1NSA BEN 2.00669
21 1C96 FLC 2.00669
22 2WPX ACO 2.00669
23 1AX2 NDG GAL 2.09205
24 3ZPG 5GP 2.34114
25 3R6K FUC GAL GLA 2.34114
26 5LUN OGA 2.34114
27 3HZT J60 2.34114
28 5OKT 9XK 2.34114
29 1F9V ADP 2.34114
30 3FXU TSU 2.34114
31 4WGF HX2 2.43902
32 4ISS TAR 2.67559
33 1F52 ADP 2.67559
34 5KOD IAC 2.67559
35 6CB2 OLC 2.73038
36 2DUR MAN MAN 2.7668
37 6BR8 6OU 2.77778
38 5VAD PRO 3.01003
39 3W54 RNB 3.01003
40 4CP8 MLI 3.01003
41 4RJD TFP 3.0303
42 3P7N FMN 3.10078
43 2GBB CIT 3.20513
44 5F7U GLC GLC 3.34448
45 4LH7 NMN 3.34448
46 1CT9 AMP 3.34448
47 2Z9I GLY ALA THR VAL 3.34448
48 2D7I UDP 3.34448
49 1HBK MYR 3.37079
50 6FLZ MMA 3.47222
51 4J25 OGA 3.49345
52 5O2D 9HH 3.5
53 6FOF LAT 3.57143
54 2Q4X HMH 3.61991
55 2F2G HMH 3.61991
56 1BGV GLU 3.67893
57 6F5W KG1 3.67893
58 4FHT DHB 3.82166
59 2BCG GER 3.8835
60 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 3.91304
61 3FS1 MYR 3.91304
62 3W5N RAM 4.01338
63 5LNW HG3 4.01338
64 4RF7 ARG 4.01338
65 3TDC 0EU 4.01338
66 3T4L ZEA 4.07407
67 5OCM 9RH 4.12371
68 4RDH AMP 4.16667
69 4RDI ATP 4.16667
70 6A56 LAT 4.26829
71 4IA6 EIC 4.34783
72 3GL0 HXX 4.34783
73 4D79 ATP 4.34783
74 6CAM BGC 4.34783
75 3UBQ SIA GAL 4.51977
76 2ZUX RAM 4.68227
77 4LWU 20U 4.70588
78 4EHQ GBL 4.72973
79 3BPX SAL 4.72973
80 5LXT GTP 4.8951
81 3I6B KDO 5
82 2WOR 2AN 5
83 5XLA SIA 5.01672
84 3ZKN WZV 5.01672
85 5Z7B VNL 5.05051
86 1RTF BEN 5.15873
87 5WSY 7UC 5.20231
88 1Y7P RIP 5.38117
89 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 5.43933
90 3B6C SDN 5.55556
91 2GJ5 VD3 5.55556
92 6BJO DUY 5.6
93 3FIU AMP 5.62249
94 1IUP ALQ 5.67376
95 3E7S AT2 5.68562
96 2QZO KN1 5.81395
97 3WUR O4B 5.84795
98 2BJ4 OHT 5.95238
99 4TV1 36M 5.9761
100 3E70 GDP 6.02007
101 4U98 ACP 6.02007
102 3KYF 5GP 5GP 6.06061
103 3HRD NIO 6.25
104 3HNB 768 6.28931
105 6F90 MVL 6.35452
106 1ZDQ MSM 6.35452
107 5U83 ZN8 6.60377
108 2AZ3 CDP 6.70732
109 5YRF GLC GLC 7.04225
110 3BY8 MLT 7.04225
111 3VY6 BGC BGC 7.0922
112 2CYB TYR 7.35786
113 1FUI FOC 7.35786
114 5W3Y ACO 7.35786
115 2J5B TYE 7.35786
116 1Y4Z PCI 7.35786
117 2GUD BMA 7.37705
118 2NUO BGC 7.37705
119 2HYQ MAN MAN 7.37705
120 2NU5 NAG 7.37705
121 2GUD MAN 7.37705
122 2HYR BGC GLC 7.37705
123 2GUC MAN 7.37705
124 2OUA AES 7.44681
125 3IX9 MTX 7.89474
126 6BTN E8M 7.92079
127 6E1Q CFA 8.02676
128 3TD3 GLY 8.13008
129 1C3M MAN MAN 8.16327
130 2D5X L35 8.21918
131 5URY PAM 8.21918
132 3KYG 5GP 5GP 8.37004
133 4NSQ COA 8.42105
134 5XQW 8EU 8.53081
135 1TV5 N8E 8.69565
136 4OGQ UMQ 8.93855
137 4OGQ 7PH 8.93855
138 4AF5 CIT 8.94737
139 2RKN LP3 9.09091
140 5IKR ID8 9.36455
141 1CM0 COA 9.52381
142 3ZVS MLI 10
143 5LX9 OLB 10.0334
144 1I7Q PYR 10.3679
145 2CYC TYR 10.7023
146 5TVI MYR 10.8696
147 4PZ6 GMP 11.0368
148 1LNX URI 11.1111
149 3H0L ADP 11.7057
150 5C8W PCG 11.8881
151 5U97 PIT 12.3746
152 1T0S BML 12.7907
153 1ID0 ANP 13.1579
154 2BVE PH5 13.4454
155 2WKQ FMN 14.0468
156 4OB6 S2T 14.0468
157 3IWD M2T 16.129
158 5NNT DPV 18.9189
159 5LWY OLB 19.3277
160 4O08 PO6 19.7324
161 6D5H FV7 20.3593
162 6D5V FVY 20.3593
163 6D5L FW7 20.3593
164 6D5J FV4 20.3593
165 6D59 FVJ 20.3593
166 6D5M FW4 20.3593
167 6D5E FVG 20.3593
168 6D55 FWA 20.3593
169 6BVK EAV 20.3593
170 6BVM EBV 20.3593
171 6D5G FVD 20.3593
172 5C9J DAO 22.2222
173 2FN1 PYR 23.7458
174 5DJT FMN 27.5862
175 5EFW FMN 27.5862
176 5Z84 CHD 38.2979
177 5ZCO CHD 38.2979
Pocket No.: 2; Query (leader) PDB : 5U3B; Ligand: 7TD; Similar sites found with APoc: 68
This union binding pocket(no: 2) in the query (biounit: 5u3b.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 5YRM BGC GLC None
2 2BS5 BGC GAL FUC None
3 2IYG FMN None
4 3ITJ CIT 1.00334
5 1FIW PBZ 1.03448
6 5C9P FUC 1.5748
7 2YVE MBT 1.62162
8 5VE5 GSH 1.67224
9 3TAO PGH 1.87266
10 1J78 OLA 2.00669
11 4NOS ITU 2.00669
12 3LL5 IP8 2.00803
13 4V3I ASP LEU THR ARG PRO 2.33463
14 6MJF SAH 2.34114
15 4RP9 ASC 2.34114
16 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 2.38095
17 5KXE 6Y2 2.46914
18 4GKY MAN 2.68199
19 4JGP PYR 2.76498
20 4PL9 ADP 3.27869
21 4ARE FLC 3.34448
22 2CJA ATP 3.34448
23 3A2Q ACA ACA 3.34448
24 1A5Z FBP 3.67893
25 3HYW DCQ 3.67893
26 4WA2 SIA GAL NAG 3.67893
27 1R37 ETX 3.67893
28 3A3B FMN 3.68421
29 5LUB 3Y7 3.81679
30 1B4N GUA 4.01338
31 3S6X SIA GAL BGC 4.34783
32 2D3S TNR 4.54545
33 1Q11 TYE 4.56989
34 5HCN DAO 4.68227
35 4Y85 499 4.68227
36 2VCN ISZ 4.98084
37 3SCH TB6 5.05051
38 1ONI BEZ 5.07246
39 5CHR 4NC 5.10949
40 4QAG F95 5.26316
41 4M44 SIA GAL NAG GAL 5.35117
42 2W5P CL8 5.36913
43 2CZL TLA 5.51471
44 3UDG TMP 5.68562
45 4CU1 71S 5.68562
46 1GYM MYG 5.7047
47 4MGA 27L 5.88235
48 4B3J COA 6.02007
49 1JBU BEN 6.34921
50 1GXU 2HP 6.59341
51 3Q8U ADP 7.00637
52 6A46 DCM 7.03125
53 5YRI GLC GLC 7.04225
54 5YRG BGC GLC 7.04225
55 5YRJ BGC GLC 7.04225
56 2PKA BEN 7.23684
57 1NW4 IMH 7.6087
58 3DUV KDO 8.01527
59 4U36 TNR 8.33333
60 4BKS X6C 8.64198
61 3O94 NCA 9.00474
62 3KCC CMP 9.23077
63 5NM7 GLY 11.2782
64 1ZEI CRS 11.3208
65 4USF 6UI 11.7057
66 1TZD ADP 12
67 5ODQ 9SB 17.3913
68 1R1Q ACE ARG GLU PTR VAL ASN VAL 19
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