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Receptor
PDB id Resolution Class Description Source Keywords
4URL 2.29 Å EC: 5.99.1.- CRYSTAL STRUCTURE OF STAPH PARE43KDA IN COMPLEX WITH KBD STAPHYLOCOCCUS AUREUS ISOMERASE ANTIBIOTICS NATURAL PRODUCT KIBDELOMYCIN GYRASTOPOISOMERASE IV
Ref.: STRUCTURES OF KIBDELOMYCIN BOUND TO STAPHYLOCOCCUS GYRB AND PARE SHOWED A NOVEL U-SHAPED BINDING MODE. ACS CHEM.BIOL. V. 9 2023 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
XAM B:2000;
A:2000;
Valid;
Valid;
none;
none;
ic50 = 500 nM
939.872 C44 H60 Cl2 N4 O14 Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4URL 2.29 Å EC: 5.99.1.- CRYSTAL STRUCTURE OF STAPH PARE43KDA IN COMPLEX WITH KBD STAPHYLOCOCCUS AUREUS ISOMERASE ANTIBIOTICS NATURAL PRODUCT KIBDELOMYCIN GYRASTOPOISOMERASE IV
Ref.: STRUCTURES OF KIBDELOMYCIN BOUND TO STAPHYLOCOCCUS GYRB AND PARE SHOWED A NOVEL U-SHAPED BINDING MODE. ACS CHEM.BIOL. V. 9 2023 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 4URL ic50 = 500 nM XAM C44 H60 Cl2 N4 O14 Cc1c(c(c([....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4URL ic50 = 500 nM XAM C44 H60 Cl2 N4 O14 Cc1c(c(c([....
50% Homology Family (50)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4URL ic50 = 500 nM XAM C44 H60 Cl2 N4 O14 Cc1c(c(c([....
2 5CTW - 55D C9 H12 N2 O2 S CCCC(=O)Nc....
3 5CTU - 54X C10 H6 N2 O S2 c1cc(sc1)c....
4 3U2D - 08B C16 H18 Br N5 O3 Cc1c(cc([n....
5 5CTX ic50 = 1.32 uM 55G C20 H13 N5 O S c1ccc(cc1)....
6 3TTZ ic50 = 0.004 uM 07N C15 H15 Cl2 F N4 O3 S Cc1c(c(c([....
7 5D6Q ic50 = 5.8 uM 57V C17 H17 N5 O S CCNC(=O)Nc....
8 3U2K - 087 C17 H18 Cl3 N5 O2 Cc1c(c(c([....
9 5D6P ic50 = 2.5 uM 57U C11 H14 N4 O2 S CCNC(=O)Nc....
10 5Z9P - AX7 C7 H7 N3 c1ccc2c(c1....
11 5D7C ic50 = 0.14 uM 57W C20 H18 N6 O CCNC(=O)Nc....
12 5CPH - EVO C14 H10 N2 O c1ccc2c(c1....
13 4WUB - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
14 4PRX - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
15 4XTJ - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
16 1EI1 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
17 4PU9 - ADP BEF n/a n/a
18 4WUC - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
19 4PRV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
20 4WUD - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
21 4ZVI Kd = 0.47 uM 4S4 C14 H11 Br2 N3 O4 c1cc(ccc1C....
22 1S16 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
23 4URN - NOV C31 H36 N2 O11 Cc1c(ccc2c....
24 4HY1 Ki = 2 nM 19X C20 H19 Cl N6 O S CCc1c(c2c(....
25 4HYM Ki = 6 nM CJC C19 H19 Cl N8 O S CCc1c(c2c(....
26 4HXW Ki = 2 nM 1A0 C19 H19 Cl N8 S CCc1c(c2c(....
27 4GFN Ki = 5 nM SUY C17 H18 Cl N7 S CCc1c(c2c(....
28 4P8O - 883 C19 H16 F N7 O CCNC(=O)Nc....
29 1KIJ - NOV C31 H36 N2 O11 Cc1c(ccc2c....
30 4B6C ic50 = 0.69 uM B5U C27 H34 N6 O2 Cc1ccc(cc1....
31 4EMV ic50 = 0.005 uM 0R9 C20 H15 F3 N6 O3 CCNC(=O)c1....
32 4MB9 - 28F C18 H20 N6 O3 S CCNC(=O)Nc....
33 4MBC - 28G C21 H24 N6 O3 S C=CCNC(=O)....
34 4LPB ic50 < 10 nM 1YP C19 H14 F3 N7 O3 S CCNC(=O)Nc....
35 4MOT - 2B7 C20 H23 N5 O2 S CC(C)CCN1c....
36 4EM7 ic50 = 7.7 uM 0RA C16 H14 N2 O2 c1cc(cc(c1....
37 5Z9Q - HX4 C9 H9 N3 c1ccc(cc1)....
38 5Z4H - AX7 C7 H7 N3 c1ccc2c(c1....
39 5Z9L - 8H8 C7 H4 F N O c1cc(c(cc1....
40 5Z9E - AX7 C7 H7 N3 c1ccc2c(c1....
41 1KZN Kd = 1.2 nM CBN C35 H37 Cl N2 O11 Cc1ccc([nH....
42 1AJ6 Kd = 1.2 uM NOV C31 H36 N2 O11 Cc1c(ccc2c....
43 5Z9B - AX7 C7 H7 N3 c1ccc2c(c1....
44 5MMO - 9JG C22 H21 N5 O3 CCNC(=O)Nc....
45 5Z4O - HX8 C12 H10 O2 c1ccc(cc1)....
46 5MMP ic50 = 0.03 uM G3Z C22 H20 N6 O CCNC(=O)Nc....
47 4DUH Kd = 6.6 uM RLI C17 H16 N4 O3 S2 CCC(=O)Nc1....
48 5MMN ic50 = 0.125 uM O54 C19 H20 N4 O CCNC(=O)Nc....
49 5Z9F - AX7 C7 H7 N3 c1ccc2c(c1....
50 4BAE ic50 = 3 nM RWX C19 H21 Br Cl N7 O4 S Cc1c(c(c([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: XAM; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 XAM 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4URL; Ligand: XAM; Similar sites found with APoc: 147
This union binding pocket(no: 1) in the query (biounit: 4url.bio2) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 1ECM TSA None
2 3ZUY TCH 0.619195
3 2OG7 AHB 1.40056
4 5OKL PAM 1.72414
5 5B0I BOG 1.74927
6 1YYE 196 1.86567
7 4F06 PHB 1.88679
8 5WGD EST 1.91571
9 5DXE EST 1.91571
10 2QA8 GEN 1.93798
11 2QZO KN1 1.93798
12 5HYR EST 1.93798
13 4MGA 27L 1.96078
14 4TUZ 36J 1.96078
15 3KP6 SAL 1.98676
16 4TV1 36M 1.99203
17 1U3R 338 2.07469
18 4G86 BNT 2.11268
19 5EE7 5MV 2.21675
20 6C1R EFD 2.21675
21 4OCT AKG 2.25225
22 4Q0A 4OA 2.31788
23 4MRP GSH 2.46305
24 4X8D AVI 2.70936
25 1TV5 N8E 2.70936
26 3NB0 G6P 2.70936
27 5H6S HDH 2.95567
28 2GFD RDA 2.9661
29 5NM7 GLY 3.00752
30 4A01 2PN 3.13316
31 5IUY BOG 3.20197
32 2O1V ADP 3.20197
33 6FS0 E4W 3.21101
34 1NF8 BOG 3.38164
35 5U5G 7VD 3.38983
36 1Z45 GAL 3.44828
37 1KZL CRM 3.84615
38 3PMA SCR 3.861
39 5H9Q TD2 3.87097
40 3WH2 FLC 4.08163
41 1FDJ 13P 4.13223
42 2HHP FLC 4.18719
43 3G5N PB2 4.18719
44 2IOR ADP 4.25532
45 4WGF HX2 4.39024
46 5N26 CPT 4.3956
47 1YOA FMN 4.40252
48 4LHD GLY 4.4335
49 4IVG ANP 4.4335
50 4IPE ANP 4.4335
51 3FAL REA 4.6798
52 1I58 ACP 4.7619
53 1I58 ADP 4.7619
54 6D28 NEC 4.92611
55 2OEM 1AE 4.92611
56 2WDA L42 4.92611
57 1YP1 LYS ASN LEU 4.9505
58 4XCL AGS 5.01931
59 1H0A I3P 5.06329
60 6CB2 OLC 5.11945
61 3KPE TM3 5.12821
62 2GBB CIT 5.12821
63 2BHW NEX 5.17241
64 5OF9 ANP 5.17241
65 1OYJ GSH 5.19481
66 5YIZ EF2 5.40541
67 5YJ0 EF2 5.40541
68 5YJ1 6EL 5.40541
69 1Q19 SSC 5.41872
70 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 5.44218
71 5I8F ML1 5.45455
72 2WR1 NAG 5.66502
73 4DE3 DN8 5.70342
74 4G6I RS3 5.71429
75 1XX4 BAM 5.74713
76 1BGQ RDC 5.77778
77 5N8V KZZ 5.7971
78 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 5.85774
79 6DIO CIT 5.91133
80 1ID0 ANP 5.92105
81 3H4L ANP 5.99455
82 1C3M MAN MAN 6.12245
83 5LX9 OLB 6.18893
84 4P7U 1PS 6.25
85 1MID LAP 6.59341
86 1Y8O ADP 6.65025
87 1Y75 NAG 6.77966
88 1DTL BEP 6.8323
89 2GWH PCI 7.04698
90 4PL9 ADP 7.10383
91 2ZKJ ADP 7.1066
92 1B63 ANP 7.20721
93 4URF 1PS 7.25806
94 1I7M PUT 7.46269
95 3E70 GDP 7.62195
96 1XVB 3BR 7.64706
97 1FMB HYB 7.69231
98 4GCZ ADP 7.88177
99 2CB8 MYA 8.04598
100 5WL1 D3D 8.08081
101 5WL1 CUY 8.08081
102 5C9J STE 8.08081
103 5OCA 9QZ 8.37438
104 2HKJ RDC 8.86699
105 4V3I ASP LEU THR ARG PRO 8.94942
106 2BCG GER 9.2233
107 5IDM ANP 9.49721
108 2VWA PTY 9.90099
109 2Q8G AZX 10.0985
110 1JGS SAL 10.1449
111 3K60 ADP 10.8374
112 4RW3 TDA 10.9272
113 4RW3 PLM 10.9272
114 1GKZ ADP 11.0825
115 4Q1A 2XZ 11.0837
116 4Q1A UDP 11.0837
117 4OGQ 7PH 11.1628
118 2XCM ADP 11.33
119 5J6A P46 11.5
120 6GMN F4E 11.5385
121 2W3L DRO 11.8056
122 2C2A ADP 12.0155
123 5IJJ I6P 12.5
124 3IHB GLU 12.5616
125 4V1F BQ1 12.7907
126 2F7A CCU 12.931
127 5F5R ANP 13.0542
128 5Y3N 8MF 13.0542
129 4BIX ADP 13.0872
130 3EHG ATP 13.2812
131 2DHC DCE 14.5161
132 1YC4 43P 14.7727
133 2I74 MAN MAN MAN MAN 15.873
134 4B7P 9UN 16.9565
135 2YI0 YI0 17.0306
136 4F4S EFO 17.1053
137 5UC4 83S 17.7273
138 1TH8 ADP 18.6207
139 1M48 FRG 19.5489
140 3EHH ADP 22.0183
141 3D36 ADP 22.1311
142 5K21 6QF 23.4043
143 1TID ATP 23.5294
144 2WOR 2AN 26
145 1ZXM ANP 31.5
146 1QZR CDX 40.4306
147 1QZR ANP 40.4306
Pocket No.: 2; Query (leader) PDB : 4URL; Ligand: XAM; Similar sites found with APoc: 9
This union binding pocket(no: 2) in the query (biounit: 4url.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 4OB6 S2T 1.72414
2 3LA3 2FT 2.46914
3 2Y7I ARG 3.49345
4 1GJW GLC 4.4335
5 2Q1A 2KT 7.50853
6 2GJ5 VD3 8.02469
7 5C9J DAO 8.08081
8 3TDC 0EU 14.2857
9 3AQT RCO 14.2857
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