Receptor
PDB id Resolution Class Description Source Keywords
1S17 1.95 Å EC: 3.5.1.88 IDENTIFICATION OF NOVEL POTENT BICYCLIC PEPTIDE DEFORMYLASE PSEUDOMONAS AERUGINOSA PEPTIDE DEFORMYLASE INHIBITOR RATIONAL DRUG DESIGN ANTIBIOPROTEIN-LIGAND COMPLEX HYDROLASE
Ref.: IDENTIFICATION OF NOVEL POTENT BICYCLIC PEPTIDE DEF INHIBITORS BIOORG.MED.CHEM.LETT. V. 14 1477 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GNR A:501;
B:601;
Valid;
Valid;
none;
none;
ic50 < 5 nM
238.263 C10 H10 N2 O3 S c1ccc...
GOL A:401;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NI A:301;
B:302;
Part of Protein;
Part of Protein;
none;
none;
submit data
58.693 Ni [Ni+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1S17 1.95 Å EC: 3.5.1.88 IDENTIFICATION OF NOVEL POTENT BICYCLIC PEPTIDE DEFORMYLASE PSEUDOMONAS AERUGINOSA PEPTIDE DEFORMYLASE INHIBITOR RATIONAL DRUG DESIGN ANTIBIOPROTEIN-LIGAND COMPLEX HYDROLASE
Ref.: IDENTIFICATION OF NOVEL POTENT BICYCLIC PEPTIDE DEF INHIBITORS BIOORG.MED.CHEM.LETT. V. 14 1477 2004
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 1S17 ic50 < 5 nM GNR C10 H10 N2 O3 S c1ccc2c(c1....
2 1IX1 - BB2 C19 H35 N3 O5 CCCCC[C@H]....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1G2A ic50 = 10 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
2 1BS8 - MET ALA SER n/a n/a
3 2AI8 ic50 = 0.16 uM SB7 C10 H15 N O2 c1ccc(cc1)....
4 1G27 ic50 = 7 nM BB1 C16 H31 N3 O4 CCCC[C@H](....
5 1LRU - BB2 C19 H35 N3 O5 CCCCC[C@H]....
6 1BS6 - MET ALA SER n/a n/a
7 1S17 ic50 < 5 nM GNR C10 H10 N2 O3 S c1ccc2c(c1....
8 1IX1 - BB2 C19 H35 N3 O5 CCCCC[C@H]....
50% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 1WS1 Ki = 0.28 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
2 1G2A ic50 = 10 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
3 1BS8 - MET ALA SER n/a n/a
4 2AI8 ic50 = 0.16 uM SB7 C10 H15 N O2 c1ccc(cc1)....
5 1G27 ic50 = 7 nM BB1 C16 H31 N3 O4 CCCC[C@H](....
6 1LRU - BB2 C19 H35 N3 O5 CCCCC[C@H]....
7 1BS6 - MET ALA SER n/a n/a
8 2EW6 ic50 = 10.8 uM Y13 C17 H17 N O4 c1cc(ccc1C....
9 2EW5 ic50 = 1.25 uM Y12 C21 H21 N O5 CC(=O)Oc1c....
10 3UWB ic50 = 10 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
11 1RL4 ic50 = 130 nM BL5 C38 H62 N8 O4 CCCC[C@@H]....
12 1S17 ic50 < 5 nM GNR C10 H10 N2 O3 S c1ccc2c(c1....
13 1IX1 - BB2 C19 H35 N3 O5 CCCCC[C@H]....
14 4DR9 ic50 = 10 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
15 3M6P Kd = 0.9 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
16 3M6R Kd = 32 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
17 3M6Q Kd = 48 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GNR; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 GNR 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1S17; Ligand: GNR; Similar sites found: 104
This union binding pocket(no: 1) in the query (biounit: 1s17.bio2) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5UGW GSH 0.001471 0.47439 None
2 2VWA PTY 0.004608 0.44789 None
3 1UY4 XYP XYP XYP XYP 0.01469 0.41494 None
4 1PVN MZP 0.01405 0.41181 None
5 2ALG DAO 0.008268 0.40065 None
6 2ALG HP6 0.008268 0.40065 None
7 2J83 BAT 0.0001072 0.48045 1.66667
8 2Q37 3AL 0.02137 0.40542 1.66667
9 1ATL 0QI 0.000009039 0.53177 2.22222
10 4XNV BUR 0.007782 0.42139 2.22222
11 3WYJ H78 0.02154 0.41881 2.22222
12 3SQP 3J8 0.01421 0.41515 2.22222
13 4B52 RDF 0.002235 0.40438 2.22222
14 2QZT PLM 0.009212 0.40773 2.7027
15 4DV8 0LX 0.0003126 0.48261 2.77778
16 4KX8 L2O VAL VAL ASP 0.0001779 0.47095 2.77778
17 3HBV ALA LYS ALA SER GLN ALA ALA 0.0001621 0.44188 2.77778
18 3G4G D71 0.006621 0.40119 2.77778
19 2YIP YIO 0.01003 0.42416 2.89855
20 3WV1 WHH 0.00006726 0.52264 2.92398
21 3Q2H QHF 0.00002282 0.50693 3.33333
22 1N4W FAD 0.01054 0.42138 3.33333
23 1BW9 PPY 0.007838 0.40878 3.33333
24 3ZJX BOG 0.02425 0.40175 3.33333
25 1MMQ RRS 0.0000105 0.51287 3.52941
26 3JUT GTQ 0.02054 0.40985 3.84615
27 1ZVX FIN 0.00006191 0.51486 3.88889
28 2Z9I GLY ALA THR VAL 0.007478 0.4349 3.88889
29 1KAP GLY SER ASN SER 0.0003612 0.42595 3.88889
30 1XM4 PIL 0.00701 0.41505 3.88889
31 1B7H LYS NLE LYS 0.01463 0.40477 3.88889
32 3TGE TGE 0.03655 0.40164 3.88889
33 4ZW3 4S9 0.0002663 0.4858 4.44444
34 2W14 WR2 0.00003328 0.4771 4.44444
35 2VJ8 HA2 0.0008367 0.46906 4.44444
36 1YP1 LYS ASN LEU 0.000005134 0.46769 4.44444
37 1NAA ABL 0.03165 0.4054 4.44444
38 1NAA 6FA 0.02331 0.405 4.44444
39 4GAA BES 0.0003868 0.44108 5
40 4AIG FLX 0.0000146 0.47376 5.55556
41 2XMY CDK 0.02938 0.41151 5.55556
42 4OYA 1VE 0.03965 0.40502 5.55556
43 5HCN DAO 0.02448 0.40101 5.55556
44 2WMC MGP 0.02109 0.42133 5.61798
45 4WZV E40 0.0000292 0.51383 5.625
46 3LXI CAM 0.002631 0.4527 6.11111
47 4BXK 1IU 0.002412 0.44428 6.11111
48 1R5L VIV 0.003074 0.42453 6.11111
49 3W68 VIV 0.002859 0.42253 6.11111
50 1G8K MGD 0.03465 0.41138 6.11111
51 5G5G MCN 0.01908 0.40263 6.11111
52 1RM8 BAT 0.00002682 0.44548 6.50888
53 1FBL HTA 0.00001885 0.46999 6.66667
54 1R55 097 0.00004874 0.44865 6.66667
55 4E28 9MZ 0.0205 0.40482 6.66667
56 1OFD FMN 0.02036 0.40029 6.66667
57 1OFD AKG 0.01835 0.40024 6.66667
58 4WKI 3PW 0.00004083 0.46612 6.80851
59 2TCL RO4 0.00001594 0.51619 7.10059
60 4AR8 IP8 GLY PRO ALA 0.000154 0.48164 7.22222
61 1J78 OLA 0.007055 0.41769 7.22222
62 4IGH 1EA 0.02821 0.41358 7.22222
63 4IGH ORO 0.02821 0.41358 7.22222
64 4IGH FMN 0.02821 0.41358 7.22222
65 1NF8 BOG 0.027 0.40346 7.22222
66 4IN9 SER TRP PHE PRO 0.00005669 0.40829 7.22892
67 5V4R MGT 0.0003007 0.49368 7.40741
68 4K90 MLA 0.01545 0.42127 7.77778
69 5BWD FUM 0.02719 0.4012 7.77778
70 2FV5 541 0.00003725 0.51852 8.33333
71 4QOM PYG 0.001896 0.42656 8.33333
72 1KUK PCA LYS TRP 0.00002004 0.47689 8.37438
73 1Q3A NGH 0.000002075 0.49145 8.48485
74 1HFS L04 0.00002632 0.52871 8.75
75 3R9V DXC 0.003028 0.44911 8.88889
76 4YMX ARG 0.01021 0.41144 8.88889
77 5X8G S0N 0.02113 0.40949 8.88889
78 2X1L MET 0.02582 0.40141 8.88889
79 3KPB SAM 0.01628 0.40263 9.01639
80 3NFD COA 0.00722 0.42326 9.15033
81 4DD8 BAT 0.00003025 0.44454 9.44444
82 3DBK RDF 0.003974 0.41073 9.44444
83 5DCH 1YO 0.01718 0.41018 9.44444
84 3HY9 098 0.00004033 0.49632 10
85 5OCA 9QZ 0.014 0.42004 10
86 3B9Z CO2 0.001821 0.47206 10.5556
87 3AHO 3A2 0.004141 0.41881 10.6383
88 1BKC INN 0.00003617 0.46936 11.1111
89 4CA5 3EF 0.001704 0.46351 11.1111
90 4ARF IP8 GLY PRO ALA 0.001171 0.42071 11.1111
91 5BSR COA 0.0202 0.41632 11.1111
92 5BSR AMP 0.01385 0.41397 11.1111
93 3I7V B4P 0.004003 0.43405 11.194
94 1JGS SAL 0.00006091 0.53914 11.5942
95 2YLN CYS 0.004008 0.44802 11.6667
96 3AB1 FAD 0.01424 0.41249 11.6667
97 3FUR Z12 0.02736 0.4025 11.6667
98 3RET SAL 0.01022 0.40346 11.8812
99 2ZXG S23 0.0002535 0.47422 13.8889
100 2Y69 CHD 0.01577 0.41221 14.2857
101 1XVB BHL 0.01389 0.41108 15
102 1BWO LPC 0.00374 0.41186 16.6667
103 4QHP 32Q 0.00251 0.42319 20
104 4UCC ZKW 0.01723 0.41399 20.5556
Pocket No.: 2; Query (leader) PDB : 1S17; Ligand: GNR; Similar sites found: 14
This union binding pocket(no: 2) in the query (biounit: 1s17.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5N53 8NB 0.02156 0.40602 None
2 2E2R 2OH 0.01059 0.41235 2.22222
3 5UC9 MYR 0.02519 0.40383 2.77778
4 5CSD ACD 0.01978 0.40388 3.77358
5 4L3L 5FI 0.01315 0.40208 3.88889
6 3KFC 61X 0.009713 0.40932 5
7 5FUS DAO 0.01356 0.40151 5.55556
8 1TV5 A26 0.01017 0.41151 6.11111
9 1TV5 N8E 0.02423 0.41097 6.11111
10 4JNA FAD 0.02741 0.40079 6.11111
11 3G9E RO7 0.01843 0.40015 11.6667
12 1OUK 084 0.04611 0.41606 12.2222
13 3TDC 0EU 0.01577 0.443 12.7778
14 2V58 LZJ 0.02758 0.40066 18.3333
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