Receptor
PDB id Resolution Class Description Source Keywords
5VRH 2.14 Å EC: 2.3.1.- APOLIPOPROTEIN N-ACYLTRANSFERASE C387S ACTIVE SITE MUTANT ESCHERICHIA COLI (STRAIN K12) LNT C387S ACYL TRANSFERASE MEMBRANE PROTEIN TRANSFERASE
Ref.: STRUCTURAL INSIGHTS INTO LIPOPROTEIN N-ACYLATION BY ESCHERICHIA COLI APOLIPOPROTEIN N-ACYLTRANSFERASE. PROC. NATL. ACAD. SCI. V. 114 E6044 2017 U.S.A.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PLM A:605;
A:604;
Valid;
Valid;
none;
none;
submit data
256.424 C16 H32 O2 CCCCC...
MG A:603;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
OLC A:608;
A:607;
Valid;
Valid;
none;
none;
submit data
356.54 C21 H40 O4 CCCCC...
OLB A:602;
A:601;
Valid;
Valid;
none;
none;
submit data
356.54 C21 H40 O4 CCCCC...
CL A:606;
Invalid;
none;
submit data
35.453 Cl [Cl-]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5VRH 2.14 Å EC: 2.3.1.- APOLIPOPROTEIN N-ACYLTRANSFERASE C387S ACTIVE SITE MUTANT ESCHERICHIA COLI (STRAIN K12) LNT C387S ACYL TRANSFERASE MEMBRANE PROTEIN TRANSFERASE
Ref.: STRUCTURAL INSIGHTS INTO LIPOPROTEIN N-ACYLATION BY ESCHERICHIA COLI APOLIPOPROTEIN N-ACYLTRANSFERASE. PROC. NATL. ACAD. SCI. V. 114 E6044 2017 U.S.A.
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 28 families.
1 5VRH - OLC C21 H40 O4 CCCCCCCCC=....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 25 families.
1 5VRH - OLC C21 H40 O4 CCCCCCCCC=....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 24 families.
1 5VRH - OLC C21 H40 O4 CCCCCCCCC=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PLM; Similar ligands found: 52
No: Ligand ECFP6 Tc MDL keys Tc
1 MYR 1 1
2 F23 1 1
3 11A 1 1
4 STE 1 1
5 KNA 1 1
6 TDA 1 1
7 DCR 1 1
8 DAO 1 1
9 DKA 1 1
10 PLM 1 1
11 F15 1 1
12 OCA 0.956522 1
13 SHV 0.833333 0.952381
14 KTC 0.793103 0.875
15 AZ1 0.73913 0.64
16 6NA 0.72 0.904762
17 NER 0.71875 0.954545
18 OLA 0.71875 0.954545
19 ELA 0.71875 0.954545
20 VCA 0.666667 0.954545
21 PAM 0.666667 0.954545
22 PML 0.625 0.6
23 3LA 0.606061 0.8
24 LEA 0.6 0.809524
25 MYZ 0.588235 0.909091
26 12H 0.586207 0.615385
27 ODD 0.567568 0.913043
28 BRC 0.566667 0.666667
29 14V 0.555556 0.740741
30 M12 0.545455 0.869565
31 14U 0.542857 0.703704
32 EIC 0.538462 0.913043
33 EOD 0.538462 0.7
34 BUA 0.48 0.666667
35 RCL 0.468085 0.84
36 HXD 0.459459 0.807692
37 56S 0.459459 0.653846
38 ODT 0.452381 0.782609
39 3X1 0.444444 0.818182
40 LNL 0.44186 0.826087
41 CNS 0.435897 0.68
42 6UL 0.435897 0.68
43 5UF 0.432432 0.807692
44 243 0.428571 0.807692
45 GYM 0.418605 0.606061
46 PL3 0.413793 0.75
47 O8N 0.413793 0.75
48 1DO 0.413793 0.75
49 F09 0.413793 0.75
50 OC9 0.413793 0.75
51 DE1 0.413793 0.75
52 T25 0.403846 0.677419
Ligand no: 2; Ligand: OLC; Similar ligands found: 63
No: Ligand ECFP6 Tc MDL keys Tc
1 OLB 1 1
2 OLC 1 1
3 MVC 0.958333 1
4 78M 0.9375 1
5 78N 0.9375 1
6 GYM 0.808511 0.969697
7 NKP 0.683333 0.688889
8 1AG 0.62069 1
9 PGW 0.597222 0.733333
10 PGV 0.589041 0.733333
11 DR9 0.589041 0.733333
12 P6L 0.581081 0.733333
13 S12 0.577465 0.627451
14 OZ2 0.573333 0.733333
15 PGM 0.571429 0.727273
16 P3A 0.558442 0.733333
17 NKN 0.533333 0.666667
18 L2C 0.525424 0.828571
19 DGA 0.525424 0.828571
20 DDR 0.525424 0.828571
21 OLA 0.519231 0.617647
22 NER 0.519231 0.617647
23 ELA 0.519231 0.617647
24 L9Q 0.5 0.603774
25 LOP 0.5 0.603774
26 VCA 0.490566 0.617647
27 PAM 0.490566 0.617647
28 ZPE 0.487179 0.603774
29 MPG 0.483871 0.941176
30 TGL 0.482759 0.722222
31 LHG 0.472222 0.711111
32 PGT 0.472222 0.711111
33 1O2 0.46988 0.711111
34 LBR 0.469697 0.805556
35 B7N 0.469136 0.607843
36 PVC 0.46875 0.815789
37 3TF 0.464286 0.711111
38 RCL 0.453125 0.705882
39 G2A 0.446429 0.882353
40 2JT 0.446429 0.882353
41 GP7 0.435294 0.603774
42 2WA 0.432836 0.885714
43 3WM 0.432836 0.885714
44 2WM 0.432836 0.885714
45 1L2 0.428571 0.711111
46 PGK 0.426829 0.666667
47 3PH 0.426471 0.630435
48 6PH 0.426471 0.630435
49 7PH 0.426471 0.630435
50 LPP 0.426471 0.630435
51 AGA 0.421053 0.711111
52 PX2 0.42029 0.608696
53 7P9 0.42029 0.630435
54 SPL 0.41791 0.608696
55 18C 0.41791 0.608696
56 16C 0.41791 0.608696
57 PEK 0.411765 0.603774
58 VA 0.40678 0.617647
59 GGD 0.40625 0.680851
60 8ND 0.405797 0.636364
61 CD4 0.405405 0.666667
62 EIC 0.4 0.647059
63 CDL 0.4 0.622222
Ligand no: 3; Ligand: OLB; Similar ligands found: 63
No: Ligand ECFP6 Tc MDL keys Tc
1 OLB 1 1
2 OLC 1 1
3 MVC 0.958333 1
4 78M 0.9375 1
5 78N 0.9375 1
6 GYM 0.808511 0.969697
7 NKP 0.683333 0.688889
8 1AG 0.62069 1
9 PGW 0.597222 0.733333
10 PGV 0.589041 0.733333
11 DR9 0.589041 0.733333
12 P6L 0.581081 0.733333
13 S12 0.577465 0.627451
14 OZ2 0.573333 0.733333
15 PGM 0.571429 0.727273
16 P3A 0.558442 0.733333
17 NKN 0.533333 0.666667
18 L2C 0.525424 0.828571
19 DGA 0.525424 0.828571
20 DDR 0.525424 0.828571
21 OLA 0.519231 0.617647
22 NER 0.519231 0.617647
23 ELA 0.519231 0.617647
24 L9Q 0.5 0.603774
25 LOP 0.5 0.603774
26 VCA 0.490566 0.617647
27 PAM 0.490566 0.617647
28 ZPE 0.487179 0.603774
29 MPG 0.483871 0.941176
30 TGL 0.482759 0.722222
31 LHG 0.472222 0.711111
32 PGT 0.472222 0.711111
33 1O2 0.46988 0.711111
34 LBR 0.469697 0.805556
35 B7N 0.469136 0.607843
36 PVC 0.46875 0.815789
37 3TF 0.464286 0.711111
38 RCL 0.453125 0.705882
39 G2A 0.446429 0.882353
40 2JT 0.446429 0.882353
41 GP7 0.435294 0.603774
42 2WA 0.432836 0.885714
43 3WM 0.432836 0.885714
44 2WM 0.432836 0.885714
45 1L2 0.428571 0.711111
46 PGK 0.426829 0.666667
47 3PH 0.426471 0.630435
48 6PH 0.426471 0.630435
49 7PH 0.426471 0.630435
50 LPP 0.426471 0.630435
51 AGA 0.421053 0.711111
52 PX2 0.42029 0.608696
53 7P9 0.42029 0.630435
54 SPL 0.41791 0.608696
55 18C 0.41791 0.608696
56 16C 0.41791 0.608696
57 PEK 0.411765 0.603774
58 VA 0.40678 0.617647
59 GGD 0.40625 0.680851
60 8ND 0.405797 0.636364
61 CD4 0.405405 0.666667
62 EIC 0.4 0.647059
63 CDL 0.4 0.622222
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5VRH; Ligand: PLM; Similar sites found: 25
This union binding pocket(no: 1) in the query (biounit: 5vrh.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4NKW PLO 0.02991 0.40411 1.21457
2 5D59 78M 0.01738 0.43805 1.65631
3 2JLD AG1 0.02917 0.41084 1.90476
4 3VRV YSD 0.03861 0.42593 2.58303
5 2A92 NAI 0.01742 0.41485 2.87356
6 4CNG SAH 0.01187 0.42579 3.13725
7 1YS4 NAP 0.04795 0.40715 3.67232
8 3T58 FAD 0.03036 0.40609 4.04624
9 1PR9 NAP 0.03201 0.40238 4.09836
10 3D3W NAP 0.03333 0.40068 4.09836
11 5KKA 6V0 0.02628 0.41782 4.80769
12 5MES 7LT 0.03458 0.40269 4.93827
13 1PL6 572 0.02646 0.41096 5.05618
14 1PL6 NAD 0.0193 0.40518 5.05618
15 2AIB ERG 0.04507 0.41107 5.10204
16 1LRI CLR 0.04325 0.40843 5.10204
17 3G4G D71 0.02182 0.40603 5.46318
18 1QG6 NAD 0.04916 0.41725 9.96169
19 1QG6 TCL 0.04916 0.41725 9.96169
20 4FC7 COA 0.03458 0.4184 10.4693
21 4FC7 NAP 0.03458 0.4184 10.4693
22 4UY1 TJM 0.008594 0.41547 10.687
23 1Q3P GLU ALA GLN THR ARG LEU 0.01694 0.42444 15.5963
24 5X8Q 82R 0.03106 0.40571 27.2727
25 2DYR TGL 0.03626 0.40185 31.9149
Pocket No.: 2; Query (leader) PDB : 5VRH; Ligand: OLB; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5vrh.bio1) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5VRH; Ligand: OLB; Similar sites found: 83
This union binding pocket(no: 3) in the query (biounit: 5vrh.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2Q2Y ADP 0.01859 0.43402 1.63488
2 2Q2Y MKR 0.01786 0.43402 1.63488
3 1IID NHM 0.01794 0.4347 1.89573
4 2RH1 CLR 0.03554 0.40192 2
5 3C9U TPP 0.04646 0.40644 2.04678
6 5MFI LYS ARG LYS ARG LYS ARG LYS ARG 0.04 0.43124 2.05761
7 5K52 OCD 0.02192 0.40908 2.10728
8 3G9E RO7 0.001988 0.48081 2.21402
9 5B4B LP5 0.02857 0.41286 2.49042
10 3KDU NKS 0.01209 0.44314 2.52708
11 4B7P 9UN 0.03769 0.42117 2.6087
12 1NTV ASN PHE ASP ASN PRO VAL TYR ARG LYS THR 0.0241 0.40849 2.63158
13 3ET3 ET1 0.02854 0.40259 2.73973
14 3ET1 ET1 0.02411 0.40318 2.74914
15 3WYJ H78 0.005606 0.4808 2.7668
16 5GIC DLC 0.03452 0.4087 2.8
17 3T03 3T0 0.006162 0.43179 2.8169
18 4ORM ORO 0.01379 0.45728 2.87356
19 4ORM 2V6 0.01379 0.45728 2.87356
20 4ORM FMN 0.01379 0.45728 2.87356
21 1KOJ PAN 0.007401 0.43174 2.87356
22 4GFD 0YB 0.008694 0.43382 2.92683
23 4FR3 LYS ARG ARG LYS SEP VAL 0.04314 0.4561 2.99145
24 4FR3 0V4 0.04314 0.4561 2.99145
25 2LBD REA 0.03426 0.4042 2.99625
26 4DM8 REA 0.02985 0.40445 3.06513
27 1XAP TTB 0.02872 0.40246 3.06513
28 1YOK P6L 0.02935 0.41941 3.44828
29 3H0A D30 0.009621 0.43647 3.50877
30 1YUC EPH 0.04373 0.40468 3.52941
31 1HN4 MJI 0.03905 0.43182 3.81679
32 2YNE YNE 0.01655 0.46191 3.90625
33 2YNE NHW 0.01655 0.46191 3.90625
34 2YNC YNC 0.005149 0.46131 3.90625
35 4XB4 45D 0.02564 0.41724 3.94737
36 4OMJ 2TX 0.01699 0.42958 3.95683
37 5B0W 22B 0.03654 0.40787 4.12371
38 3KRO DST 0.02119 0.41601 4.40678
39 3KRO IPE 0.02119 0.41601 4.40678
40 4UWJ 7L5 0.02207 0.44557 4.914
41 4UWJ MYA 0.02207 0.44557 4.914
42 3HP9 CF1 0.004274 0.42594 4.98084
43 3E85 BSU 0.01313 0.44163 5.06329
44 4LY9 1YY 0.025 0.43489 5.55556
45 4LY9 S6P 0.0235 0.43489 5.55556
46 5CSD ACD 0.01212 0.43998 5.66038
47 1IYK MYA 0.007715 0.44667 5.86735
48 3ANP DAO 0.007007 0.4404 5.88235
49 3ANP DCC 0.01555 0.42623 5.88235
50 3FAL LO2 0.03933 0.40707 5.9387
51 3FAL REA 0.01991 0.40247 5.9387
52 3ZLR X0B 0.01554 0.43643 6.32911
53 3KFC 61X 0.03364 0.41109 6.71937
54 5AAV GW5 0.04138 0.42385 6.74603
55 2J8C U10 0.007581 0.47295 7.11744
56 2J8C SPO 0.007581 0.47295 7.11744
57 1RQJ RIS 0.02174 0.41387 7.35786
58 5OCA 9QZ 0.0008659 0.46488 7.47126
59 1FCH TYR GLN SER LYS LEU 0.01276 0.4288 8.15217
60 4MNS 2AX 0.02009 0.43738 8.1761
61 4DXJ 0M9 0.04607 0.40159 8.83978
62 3QKD HI0 0.01113 0.4307 9.39227
63 1XVB 3BR 0.009186 0.41554 9.41177
64 1UVC STE 0.004335 0.45531 10.989
65 4RC8 STE 0.01487 0.41989 11.2613
66 1L6O SER LEU LYS LEU MET THR THR VAL 0.006834 0.43325 11.5789
67 5CYV WCA 0.01688 0.41934 11.6438
68 1KJM ALA GLN PHE SER ALA SER ALA SER ARG 0.002761 0.46956 16
69 1MHC FME TYR PHE ILE ASN ILE LEU THR LEU 0.001561 0.48826 16.1616
70 3SCM LGN 0.01146 0.45565 16.1616
71 3QUZ QUV 0.03116 0.42945 16.1616
72 3G08 FEE 0.04879 0.41955 16.1616
73 1FO0 ILE ASN PHE ASP PHE ASN THR ILE 0.03405 0.41931 16.1616
74 2DYR PGV 0.009548 0.4469 31.9149
75 5JHD GLY ILE LEU GLY PHE VAL PHE THR LEU 0.01042 0.44771 32
76 3KYO LYS LEU PRO ALA GLN PHE TYR ILE LEU 0.006167 0.44705 32
77 2X4T ASN LEU VAL PRW MET VAL ALA THR VAL 0.009258 0.43589 32
78 5C0C ARG GLN PHE GLY PRO ASP TRP ILE VAL ALA 0.02925 0.42738 32
79 1OGA GLY ILE LEU GLY PHE VAL PHE THR LEU 0.04804 0.41583 32
80 5U98 1KX 0.0157 0.43891 32.3232
81 5U98 VAL THR THR ASP ILE GLN VAL LYS VAL 0.01497 0.42958 32.3232
82 5L2J 70E 0.02247 0.44502 32.6531
83 5L2J 6UL 0.02144 0.44502 32.6531
Pocket No.: 4; Query (leader) PDB : 5VRH; Ligand: OLC; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5vrh.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5VRH; Ligand: OLC; Similar sites found: 1
This union binding pocket(no: 5) in the query (biounit: 5vrh.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4HGD KGT 0.001707 0.43249 4.98084
Pocket No.: 6; Query (leader) PDB : 5VRH; Ligand: PLM; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5vrh.bio1) has 3 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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