Receptor
PDB id Resolution Class Description Source Keywords
3P3E 1.28 Å EC: 3.5.1.- CRYSTAL STRUCTURE OF THE PSEUDOMONAS AERUGINOSA LPXC/LPC-009 PSEUDOMONAS AERUGINOSA LIPID A BIOSYNTHESIS LIPID A SYNTHESIS LPXC BAAB SANDWICHHYDROLASE DEACETYLATION ANTIBIOTIC ACYL UDP-GLCNAC HYDRLPC-009
Ref.: SPECIES-SPECIFIC AND INHIBITOR-DEPENDENT CONFORMATI LPXC: IMPLICATIONS FOR ANTIBIOTIC DESIGN. CHEM.BIOL. V. 18 38 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3P3 A:501;
Valid;
none;
submit data
362.379 C21 H18 N2 O4 C[C@H...
NA A:601;
Invalid;
none;
submit data
22.99 Na [Na+]
NO3 A:701;
A:702;
A:703;
A:704;
A:705;
A:706;
A:707;
A:708;
A:709;
A:710;
A:711;
A:712;
A:713;
A:714;
A:715;
A:716;
A:717;
A:718;
A:719;
A:720;
A:721;
A:722;
A:723;
A:724;
A:725;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.005 N O3 [N+](...
ZN A:400;
A:401;
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 27 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 25 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: 3P3; Similar ligands found: 14
No: Ligand ECFP6 Tc MDL keys Tc
1 3P3 1 1
2 ZH2 0.754098 0.913043
3 5EP 0.557143 0.75
4 L53 0.528571 0.791667
5 ZH4 0.513158 0.791667
6 C90 0.5 0.677419
7 1WM 0.487179 0.854167
8 5EM 0.465753 0.764706
9 5EN 0.435897 0.807692
10 P76 0.421687 0.666667
11 1WN 0.411765 0.84
12 UKW 0.405797 0.818182
13 1JS 0.4 0.696429
14 1WL 0.4 0.644068
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5U3B; Ligand: 7TD; Similar sites found: 49
This union binding pocket(no: 1) in the query (biounit: 5u3b.bio2) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1M2Z BOG 0.002862 0.47508 None
2 4WG0 CHD 0.009369 0.43619 None
3 5HWK BEZ 0.02061 0.41823 None
4 1YXM ADE 0.03183 0.40177 1.67224
5 3ZJX BOG 0.03262 0.40779 1.7301
6 2BTM PGA 0.03 0.40543 1.98413
7 4WCX ALA 0.01278 0.42091 2.00669
8 1NSA BEN 0.01826 0.41637 2.00669
9 2WPX ACO 0.01224 0.4035 2.00669
10 3HZT J60 0.02013 0.41048 2.34114
11 4ISS TAR 0.03178 0.40993 2.67559
12 1F52 ADP 0.01767 0.40955 2.67559
13 5VAD PRO 0.01195 0.41415 3.01003
14 3P7N FMN 0.006121 0.41708 3.10078
15 2GBB CIT 0.021 0.41774 3.20513
16 4LH7 NMN 0.02646 0.41322 3.34448
17 4J25 OGA 0.02087 0.41849 3.49345
18 2BCG GER 0.01867 0.41616 3.8835
19 4RDH AMP 0.01469 0.40634 4.16667
20 3GL0 HXX 0.008406 0.42547 4.34783
21 4LWU 20U 0.01576 0.40835 4.70588
22 3ZKN WZV 0.03868 0.40352 5.01672
23 3B6C SDN 0.003221 0.46095 5.55556
24 5EW9 5VC 0.002951 0.44999 5.90406
25 4U98 ACP 0.009042 0.41629 6.02007
26 3HNB 768 0.03275 0.41935 6.28931
27 5U83 ZN8 0.03437 0.40628 6.60377
28 3BY8 MLT 0.04476 0.40505 7.04225
29 3VY6 BGC BGC 0.01122 0.44551 7.0922
30 1GMN IDS SGN IDS SGN IDS 0.03934 0.40577 7.10383
31 2CYB TYR 0.001152 0.48666 7.35786
32 2J5B TYE 0.03066 0.40375 7.35786
33 2NU5 NAG 0.03335 0.41436 7.37705
34 2GUC MAN 0.03585 0.41056 7.37705
35 3IX9 MTX 0.0166 0.40384 7.89474
36 1TV5 N8E 0.03094 0.41593 8.69565
37 2RKN LP3 0.01245 0.41329 9.09091
38 5IKR ID8 0.01762 0.40961 9.36455
39 1CM0 COA 0.01836 0.40515 9.52381
40 3ZVS MLI 0.04336 0.40085 10
41 5LX9 OLB 0.004585 0.43418 10.0334
42 2CYC TYR 0.01108 0.43368 10.7023
43 1LNX URI 0.0451 0.40253 11.1111
44 1T0S BML 0.01741 0.41393 12.7907
45 1ID0 ANP 0.01067 0.42037 13.1579
46 2BVE PH5 0.03797 0.40206 13.4454
47 5LWY OLB 0.004686 0.43373 19.3277
48 2FN1 PYR 0.01488 0.42921 23.7458
49 5EFW FMN 0.01212 0.40368 27.5862
Pocket No.: 2; Query (leader) PDB : 5U3B; Ligand: 7TD; Similar sites found: 18
This union binding pocket(no: 2) in the query (biounit: 5u3b.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5VE5 GSH 0.03027 0.40622 1.67224
2 4NOS ITU 0.02594 0.40993 2.00669
3 3LL5 IP8 0.02055 0.42151 2.00803
4 4V3I ASP LEU THR ARG PRO 0.01961 0.42055 2.33463
5 4WGF HX2 0.03048 0.41727 2.43902
6 4JGP PYR 0.01197 0.43327 2.76498
7 4WA2 SIA GAL NAG 0.04167 0.40342 3.67893
8 1B4N GUA 0.02718 0.41276 4.01338
9 5HCN DAO 0.02883 0.41158 4.68227
10 2W5P CL8 0.04455 0.40153 5.36913
11 1Y7P RIP 0.005249 0.40244 5.38117
12 4MGA 27L 0.03514 0.40838 5.88235
13 2NUO BGC 0.03253 0.42281 7.37705
14 1NW4 IMH 0.03339 0.40418 7.6087
15 3DUV KDO 0.04459 0.40135 8.01527
16 4BKS X6C 0.03412 0.4088 8.64198
17 3O94 NCA 0.03331 0.41221 9.00474
18 1TZD ADP 0.01936 0.41513 12
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