Receptor
PDB id Resolution Class Description Source Keywords
4YRD 2.44 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF CAPF WITH INHIBITOR 3-ISOPROPENYL-TROPO STAPHYLOCOCCUS AUREUS (STRAIN MU50 / A700699) CAPF CUPIN CAPSULAR POLYSACCHARIDE STAPHYLOCOCCUS AUREUS OXIDOREDUCTASE-INHIBITOR COMPLEX
Ref.: DISCOVERY AND CHARACTERIZATION OF NATURAL TROPOLONE INHIBITORS OF THE ANTIBACTERIAL TARGET CAPF FROM STAPHYLOCOCCUS AUREUS. SCI REP V. 5 15337 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN A:401;
B:401;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
3IT B:402;
A:402;
Valid;
Valid;
none;
none;
Kd = 27 uM
162.185 C10 H10 O2 CC(=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4YRD 2.44 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF CAPF WITH INHIBITOR 3-ISOPROPENYL-TROPO STAPHYLOCOCCUS AUREUS (STRAIN MU50 / A700699) CAPF CUPIN CAPSULAR POLYSACCHARIDE STAPHYLOCOCCUS AUREUS OXIDOREDUCTASE-INHIBITOR COMPLEX
Ref.: DISCOVERY AND CHARACTERIZATION OF NATURAL TROPOLONE INHIBITORS OF THE ANTIBACTERIAL TARGET CAPF FROM STAPHYLOCOCCUS AUREUS. SCI REP V. 5 15337 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 4YRD Kd = 27 uM 3IT C10 H10 O2 CC(=C)C1=C....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 4YRD Kd = 27 uM 3IT C10 H10 O2 CC(=C)C1=C....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 4YRD Kd = 27 uM 3IT C10 H10 O2 CC(=C)C1=C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 3IT; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 3IT 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4YRD; Ligand: 3IT; Similar sites found: 124
This union binding pocket(no: 1) in the query (biounit: 4yrd.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5A3T MMK 0.001161 0.47998 1.39276
2 2WBP ZZU 0.007976 0.41524 1.39665
3 2WBP SIN 0.007976 0.41524 1.39665
4 4NTM 2K8 0.009999 0.41603 1.65289
5 1ZOA 140 0.0122 0.42748 1.67131
6 1GP6 DH2 0.002341 0.45136 1.68539
7 1GP6 SIN 0.002341 0.45136 1.68539
8 1GP6 QUE 0.002494 0.45136 1.68539
9 2I6A 5I5 0.01515 0.41244 1.73913
10 2ARC ARA 0.006484 0.40982 1.82927
11 3Q9T FAY 0.04476 0.41009 1.94986
12 5AYE BMA BMA 0.01211 0.40886 2.08955
13 2JFN GLU 0.01034 0.4164 2.10526
14 2B4G FMN 0.02416 0.4141 2.2082
15 5F3I 5UJ 0.003128 0.47864 2.22841
16 2YBP 2HG 0.0006311 0.46581 2.22841
17 2OS2 OGA 0.0008773 0.45316 2.22841
18 5FWE OGA 0.0008811 0.45283 2.22841
19 4PIV 2W4 0.009727 0.42479 2.22841
20 5LY2 OGA 0.00242 0.42429 2.22841
21 2P5B OGA 0.0007279 0.46557 2.27273
22 2Q8E OGA 0.0009013 0.45394 2.27273
23 2Q8C AKG 0.0007112 0.43064 2.27273
24 1DRY AKG 0.005882 0.43498 2.46914
25 1DRY AAG 0.005882 0.43498 2.46914
26 3AVS OGA 0.0002363 0.48868 2.50696
27 3AVR OGA 0.0002136 0.48328 2.50696
28 4PAB THG 0.02625 0.40561 2.50696
29 3LPP KTL 0.01796 0.40259 2.50696
30 4N14 WR7 0.0007323 0.43747 2.54777
31 2RDQ AKG 0.002599 0.45152 2.77778
32 5FP3 3JI 0.0001616 0.51619 2.78552
33 5KR7 6X9 0.0004078 0.47303 2.78552
34 3L4U DSK 0.009989 0.42601 2.78552
35 4A0M NAD 0.01582 0.4186 2.78552
36 4ZAC 4LU 0.02392 0.40463 2.78552
37 4HJY NAG NAG NAG 0.02282 0.42202 2.91262
38 1H5Q NAP 0.03325 0.41335 3.01887
39 2X3N FAD 0.0382 0.41767 3.06407
40 3S2U UD1 0.01777 0.4026 3.06407
41 1XQP 8HG 0.01167 0.41502 3.125
42 1OS7 TAU 0.008907 0.41384 3.18021
43 1OS7 AKG 0.008907 0.41384 3.18021
44 4AGQ P96 0.009896 0.42592 3.19635
45 4NPL AKG 0.0001066 0.50789 3.2
46 3RDO BTN 0.01422 0.40809 3.26797
47 1OLT SAM 0.01616 0.40643 3.34262
48 2JLD AG1 0.04048 0.40313 3.34262
49 4RFR RHN 0.005912 0.42799 3.44828
50 4QM9 CYS 0.00002343 0.53977 3.46821
51 4EES FMN 0.008935 0.41838 3.47826
52 5I0U DCY 0.000005056 0.5736 3.5
53 2FCU AKG 0.002414 0.42602 3.51438
54 4OCT AKG 0.00007744 0.51722 3.6036
55 3KV4 OGA 0.001279 0.44539 3.62117
56 3OPT AKG 0.00136 0.4092 3.62117
57 1O68 KIV 0.002891 0.4258 3.63636
58 1RYA GDP 0.02104 0.4185 3.75
59 5DQ8 FLF 0.04186 0.40857 3.75
60 3JRS A8S 0.01052 0.41617 3.84615
61 5FWJ MMK 0.002117 0.43779 3.89972
62 3N9O OGA 0.004715 0.41259 3.89972
63 5MM0 GDD 0.02576 0.4124 3.89972
64 3N9Q OGA 0.006174 0.40854 3.89972
65 3N9P OGA 0.006734 0.40043 3.89972
66 5IVE 6E8 0.002209 0.45976 3.93939
67 2ADA HPR 0.00136 0.46343 3.97727
68 1Q8Y ADP 0.02436 0.40209 4.17827
69 1N62 MCN 0.0494 0.40065 4.21687
70 4R38 RBF 0.005604 0.43043 4.28571
71 4P7X YCP 0.01447 0.4 4.45205
72 4P7X AKG 0.01447 0.4 4.45205
73 4Y3O OGA 0.004978 0.41074 4.45682
74 2AMT GPP 0.02698 0.40413 4.45682
75 4CCK OGA 0.006552 0.40367 4.45682
76 2YAK OSV 0.02675 0.40944 4.5614
77 5FLJ QUE 0.0002668 0.50775 4.83871
78 1YRO GDU 0.04323 0.41148 4.87805
79 4M26 ZZU 0.009637 0.42014 4.94506
80 4M26 SIN 0.009637 0.42014 4.94506
81 4XF6 LIP 0.0443 0.40075 5.12821
82 4XF6 ADP 0.04767 0.40075 5.12821
83 4XF6 INS 0.0443 0.40075 5.12821
84 4N70 2HX 0.0277 0.4265 5.18293
85 4NJH SAM 0.01604 0.41931 5.21739
86 4NJH 2K8 0.01604 0.41931 5.21739
87 1LF9 ACR 0.02212 0.40112 5.29248
88 4RW3 IPD 0.0131 0.40496 5.29801
89 4GJY OGA 0.000209 0.46505 5.95745
90 4WUJ FMN 0.0135 0.41181 6.12245
91 2Z6D FMN 0.01137 0.40739 6.15385
92 1GQG DCD 0.0002437 0.50889 6.85714
93 5OO5 UUA 0.0005083 0.48081 7.25806
94 4QXB OGA 0.006654 0.40923 7.35294
95 5HV0 AKG 0.0003355 0.48885 7.37327
96 5HCY 60D 0.04516 0.40721 7.85498
97 2JIG PD2 0.001002 0.45937 8.03571
98 3ZDS HMQ 0.005289 0.40388 8.07799
99 3ZDS OMD 0.005033 0.40374 8.07799
100 3ZDS HQ9 0.004584 0.40196 8.07799
101 1NYW DAU 0.0007341 0.47537 8.62944
102 4JGX PLM 0.01554 0.40995 9.30233
103 5X1M THG 0.02741 0.41289 9.47075
104 5JSP DQY 0.000006199 0.56687 10.4478
105 4HN1 TYD 0.01176 0.41957 10.4478
106 3MPB FRU 0.00004016 0.53082 10.9756
107 2IXC TRH 0.01029 0.41171 11.3861
108 4ZU4 4TG 0.0000008794 0.63109 11.4865
109 2PVN P63 0.03919 0.4051 11.9318
110 1J3R 6PG 0.0009695 0.43657 12.1053
111 2GC0 PAN 0.0003881 0.46985 12.234
112 1U7Z PMT 0.03242 0.41849 12.3894
113 2Z6C FMN 0.002967 0.44887 12.4031
114 5U55 S0H 0.01742 0.40005 13.6842
115 4IE6 UN9 0.001154 0.4643 15.8774
116 1L2T ATP 0.02637 0.40319 16.1702
117 3FW4 CAQ 0.005137 0.45528 16.8539
118 3B1Q NOS 0.01961 0.40461 17.1779
119 5TFZ 7BC 0.000004407 0.57741 20
120 1NCQ W11 0.0005124 0.48376 20.5882
121 3LDQ 3P1 0.03112 0.40861 22.807
122 3DZ6 PUT 0.003003 0.41196 25.3731
123 1LRH NLA 0.00016 0.50329 25.7669
124 2XUM OGA 0.0004115 0.4553 40
Pocket No.: 2; Query (leader) PDB : 4YRD; Ligand: 3IT; 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: 4yrd.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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