Receptor
PDB id Resolution Class Description Source Keywords
4URN 2.3 Å EC: 5.99.1.- CRYSTAL STRUCTURE OF STAPH PARE 24KDA IN COMPLEX WITH NOVOBI STAPHYLOCOCCUS AUREUS ISOMERASE ANTIBIOTICS GYRASE NATURAL PRODUCT
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
NOV C:2000;
B:2000;
A:2000;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
612.624 C31 H36 N2 O11 Cc1c(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4URN 2.3 Å EC: 5.99.1.- CRYSTAL STRUCTURE OF STAPH PARE 24KDA IN COMPLEX WITH NOVOBI STAPHYLOCOCCUS AUREUS ISOMERASE ANTIBIOTICS GYRASE NATURAL PRODUCT
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 4URN - NOV C31 H36 N2 O11 Cc1c(ccc2c....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 4URN - NOV C31 H36 N2 O11 Cc1c(ccc2c....
2 4LP0 ic50 < 10 nM 1YM C18 H14 F3 N5 O3 S CCNC(=O)Nc....
3 4EMV ic50 = 0.005 uM 0R9 C20 H15 F3 N6 O3 CCNC(=O)c1....
4 4MB9 - 28F C18 H20 N6 O3 S CCNC(=O)Nc....
5 4MBC - 28G C21 H24 N6 O3 S C=CCNC(=O)....
6 4LPB ic50 < 10 nM 1YP C19 H14 F3 N7 O3 S CCNC(=O)Nc....
7 4MOT - 2B7 C20 H23 N5 O2 S CC(C)CCN1c....
8 4EM7 ic50 = 7.7 uM 0RA C16 H14 N2 O2 c1cc(cc(c1....
50% Homology Family (35)
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 5CTX ic50 = 1.32 uM 55G C20 H13 N5 O S c1ccc(cc1)....
5 3TTZ ic50 = 0.004 uM 07N C15 H15 Cl2 F N4 O3 S Cc1c(c(c([....
6 5D6Q ic50 = 5.8 uM 57V C17 H17 N5 O S CCNC(=O)Nc....
7 3U2K - 087 C17 H18 Cl3 N5 O2 Cc1c(c(c([....
8 5D6P ic50 = 2.5 uM 57U C11 H14 N4 O2 S CCNC(=O)Nc....
9 5D7C ic50 = 0.14 uM 57W C20 H18 N6 O CCNC(=O)Nc....
10 5CPH - EVO C14 H10 N2 O c1ccc2c(c1....
11 4WUB - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
12 4PRX - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
13 4XTJ - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
14 1EI1 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
15 4PU9 - ADP BEF n/a n/a
16 4WUC - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
17 4PRV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
18 4WUD - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
19 4ZVI Kd = 0.47 uM 4S4 C14 H11 Br2 N3 O4 c1cc(ccc1C....
20 1S16 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
21 4URN - NOV C31 H36 N2 O11 Cc1c(ccc2c....
22 4HY1 Ki = 2 nM 19X C20 H19 Cl N6 O S CCc1c(c2c(....
23 4HYM Ki = 6 nM CJC C19 H19 Cl N8 O S CCc1c(c2c(....
24 1KZN Kd = 1.2 nM CBN C35 H37 Cl N2 O11 Cc1ccc([nH....
25 1AJ6 Kd = 1.2 uM NOV C31 H36 N2 O11 Cc1c(ccc2c....
26 5MMP ic50 = 0.03 uM G3Z C22 H20 N6 O CCNC(=O)Nc....
27 4DUH Kd = 6.6 uM RLI C17 H16 N4 O3 S2 CCC(=O)Nc1....
28 5MMN ic50 = 0.125 uM O54 C19 H20 N4 O CCNC(=O)Nc....
29 1KIJ - NOV C31 H36 N2 O11 Cc1c(ccc2c....
30 4LP0 ic50 < 10 nM 1YM C18 H14 F3 N5 O3 S CCNC(=O)Nc....
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 4MOT - 2B7 C20 H23 N5 O2 S CC(C)CCN1c....
34 4EM7 ic50 = 7.7 uM 0RA C16 H14 N2 O2 c1cc(cc(c1....
35 4BAE ic50 = 3 nM RWX C19 H21 Br Cl N7 O4 S Cc1c(c(c([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NOV; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 NOV 1 1
2 CBN 0.669291 0.820895
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4URN; Ligand: NOV; Similar sites found: 167
This union binding pocket(no: 1) in the query (biounit: 4urn.bio2) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2B4D COA 0.006633 0.43186 None
2 1H0A I3P 0.006495 0.42024 None
3 5DXE EST 0.01371 0.40799 None
4 3UUD EST 0.01403 0.40749 None
5 2QA8 GEN 0.01424 0.40715 None
6 4TUZ 36J 0.0129 0.4071 None
7 2QZO KN1 0.0194 0.40619 None
8 1NZY BCA 0.03445 0.40501 None
9 4MGB XDH 0.01943 0.40433 None
10 4TV1 36M 0.01088 0.40323 None
11 4MG7 27H 0.02115 0.40245 None
12 2BJ4 OHT 0.02688 0.40063 None
13 4XCL AGS 0.0002512 0.50448 1.33333
14 3L0E G58 0.01882 0.41769 1.33333
15 5HYR EST 0.01474 0.4064 1.33333
16 2G86 UMP 0.006593 0.46423 1.77778
17 3MBG FAD 0.02484 0.40996 2.15827
18 1BGQ RDC 0.0006573 0.49425 2.22222
19 1IZE IVA VAL VAL STA ALA STA 0.005332 0.44193 2.22222
20 3KFC 61X 0.02796 0.41458 2.22222
21 3U5S FAD 0.01918 0.40986 2.38095
22 3O55 FAD 0.02472 0.41007 2.4
23 2CNT COA 0.008432 0.43159 2.5
24 1WWZ ACO 0.005537 0.44712 2.51572
25 1JR8 FAD 0.01419 0.41826 2.5641
26 5FM0 WAQ 0.01267 0.43311 2.66667
27 1XAP TTB 0.01513 0.41349 2.66667
28 5KOR GDP 0.02202 0.4051 2.66667
29 5K53 STE 0.0275 0.40012 2.66667
30 3GYT DL4 0.01969 0.41239 3.11111
31 2E2R 2OH 0.04744 0.40417 3.11111
32 4RC8 STE 0.01933 0.41128 3.15315
33 2VZZ SCA 0.008904 0.43756 3.21101
34 1UVC STE 0.03787 0.4028 3.2967
35 4IVG ANP 0.0004359 0.49827 3.55556
36 3L9R L9R 0.03438 0.41079 3.55556
37 2O3Z AI7 0.03693 0.41014 3.55556
38 3BQ5 HCS 0.0436 0.40816 3.55556
39 4KOT CE3 0.007249 0.45175 3.7037
40 4RI1 ACO 0.0208 0.40638 3.76344
41 1TIQ COA 0.003562 0.43729 3.88889
42 4B5P ACO 0.0005621 0.49782 4
43 3DST GRG 0.01545 0.45713 4
44 1ZAP A70 0.008328 0.4391 4
45 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.00537 0.4368 4
46 3G9E RO7 0.0124 0.43477 4
47 5TWO 7MV 0.00735 0.42958 4
48 1XAJ CRB 0.02624 0.42494 4
49 1XAJ NAD 0.02624 0.42494 4
50 3FUR Z12 0.03876 0.41798 4
51 5LWV UDP 0.03264 0.40626 4
52 2HFP NSI 0.02992 0.40288 4
53 2IOR ADP 0.00004956 0.51672 4.44444
54 2Z7I 742 0.04126 0.429 4.44444
55 5U5G 7VD 0.006007 0.41577 4.44444
56 3PMA SCR 0.00701 0.40257 4.44444
57 1I58 ADP 0.00002379 0.5458 4.7619
58 1I58 ACP 0.0001785 0.51424 4.7619
59 1NF8 BOG 0.0109 0.4101 4.83092
60 4BIX ADP 0.001876 0.44029 4.88889
61 5HGR 45D 0.01977 0.42492 4.88889
62 1TV5 N8E 0.01081 0.41654 4.88889
63 1ZSQ PIB 0.019 0.41007 4.88889
64 2AX9 BHM 0.04803 0.40858 4.88889
65 5B4B LP5 0.03456 0.40615 4.88889
66 4XPL ACO 0.00803 0.42382 4.90798
67 3QCP FAD 0.01711 0.41849 5.33333
68 1DB1 VDX 0.0302 0.41277 5.33333
69 3OLL EST 0.01331 0.4107 5.33333
70 1U3R 338 0.01586 0.40881 5.33333
71 2YJD YJD 0.01621 0.40638 5.33333
72 1M13 HYF 0.04222 0.40377 5.33333
73 1YYE 196 0.01673 0.40364 5.33333
74 5FVJ ACO 0.00463 0.44977 5.42169
75 3EHH ADP 0.007948 0.4126 5.50459
76 3FV3 IVA VAL VAL STA ALA STA 0.003402 0.4568 5.60472
77 5ECP ATP 0.03466 0.41646 5.77778
78 5ECP MET 0.03337 0.41646 5.77778
79 5ECP JAA 0.03337 0.41646 5.77778
80 1ZDU P3A 0.025 0.40981 5.77778
81 5IBE 69M 0.04938 0.40517 5.77778
82 2GGH NLQ 0.01998 0.40179 5.77778
83 1ID0 ANP 0.0008647 0.46539 5.92105
84 5LLT DND 0.04517 0.40217 6.10329
85 3FEI CTM 0.009927 0.4279 6.22222
86 4TXJ THM 0.03172 0.42205 6.22222
87 4DE9 VTP 0.0307 0.41011 6.22222
88 5IXK 6EW 0.03432 0.40865 6.22222
89 2Q1H AS4 0.02028 0.4052 6.22222
90 5APK 76E 0.04075 0.4011 6.22222
91 4KVX ACO 0.02285 0.41322 6.41026
92 5HBN RPI 0.01214 0.40358 6.41026
93 2Q4V ACO 0.005749 0.44335 6.47059
94 1KOL NAD 0.03335 0.41457 6.66667
95 2ZPA ACO 0.01682 0.41442 6.66667
96 1XIU REA 0.0225 0.40108 6.66667
97 3LF0 ATP 0.02831 0.40264 7.01754
98 3LN0 52B 0.00373 0.46957 7.11111
99 2KCE D16 0.02236 0.42879 7.11111
100 1SR7 MOF 0.02663 0.4146 7.11111
101 4GFD 0YB 0.01611 0.41695 7.31707
102 4UA3 COA 0.003973 0.44325 8.24742
103 3FAL LO2 0.0339 0.40894 8.44444
104 4M8E 29V 0.02797 0.40291 8.44444
105 3NRR UMP 0.03933 0.40192 8.44444
106 4POJ 2VP 0.03218 0.40121 8.44444
107 1QY8 RDI 0.0001768 0.50503 8.88889
108 3TDC 0EU 0.03627 0.40915 8.88889
109 4H6U ACO 0.003037 0.45109 9
110 4CVZ TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 0.01027 0.4414 9.18367
111 4R6W PC 0.04384 0.4201 9.33333
112 2VL8 CTS 0.0115 0.41961 9.33333
113 5BNS 4VM 0.02494 0.40987 9.33333
114 5GK9 ACO 0.02693 0.40943 9.33333
115 5O4J PJL 0.04537 0.40421 9.33333
116 3EHG ATP 0.003073 0.40685 9.375
117 1JGS SAL 0.00008463 0.49384 9.42029
118 4IEH 1E9 0.02698 0.40523 9.46746
119 5IDM ANP 0.00004811 0.53609 9.49721
120 4LO2 GAL BGC 0.006921 0.4084 9.77778
121 3ORF NAD 0.04465 0.40132 9.77778
122 5JHD GLY ILE LEU GLY PHE VAL PHE THR LEU 0.04586 0.40881 10
123 3DBX PLM 0.007054 0.42016 10.101
124 5U98 1KX 0.04931 0.41978 10.101
125 5U98 VAL THR THR ASP ILE GLN VAL LYS VAL 0.0266 0.41346 10.101
126 5L2J 6UL 0.0383 0.42916 10.2041
127 5L2J 70E 0.04009 0.42916 10.2041
128 5ISZ GLY ILE LEU GLY PHE VAL PHE THR LEU 0.03476 0.41358 10.2041
129 3H4L ANP 0.00007075 0.53485 10.2222
130 2GFD RDA 0.0002756 0.50858 10.2222
131 2WR1 NAG 0.0001392 0.48451 10.2222
132 5K04 COA 0.007992 0.43117 10.2222
133 4PJT 2YQ 0.01658 0.42566 10.2222
134 4XNV BUR 0.01291 0.40166 10.2222
135 2W90 6PG 0.02562 0.40786 11.1111
136 4XOQ F42 0.01527 0.42637 11.5942
137 1Y8O ADP 0.000006647 0.56665 12
138 1YMT DR9 0.02573 0.41178 12
139 2ZKJ ADP 0.00006555 0.56389 12.8889
140 2C2A ADP 0.0001922 0.50573 13.7778
141 4GCZ ADP 0.006012 0.43019 14.2222
142 2VCH UDP 0.03503 0.40462 14.2222
143 4RW3 TDA 0.005861 0.43635 14.6667
144 4RW3 PLM 0.01416 0.41124 14.6667
145 4B7P 9UN 0.0002457 0.53966 15.5556
146 2NU8 COA 0.0148 0.4232 15.5556
147 2HKJ RDC 0.00008092 0.54374 16
148 2O1V ADP 0.0001207 0.50471 16.4444
149 3NT6 COA 0.009579 0.43962 16.8889
150 1YC4 43P 0.00008766 0.51464 17.3333
151 3NTD COA 0.01182 0.43588 17.3333
152 3NMQ 7PP 0.0004759 0.4313 17.7778
153 1OQC FAD 0.01947 0.41265 18.4
154 1GKZ ADP 0.00002363 0.55433 18.6667
155 3K60 ADP 0.0007249 0.46029 19.5556
156 5DEY 59T 0.03457 0.41272 19.5556
157 2XCM ADP 0.00008983 0.4622 20.4444
158 1GHE ACO 0.01218 0.42328 21.4689
159 1TH8 ADP 0.0001409 0.50141 22.069
160 3D36 ADP 0.0005044 0.48685 22.1311
161 5F5R ANP 0.0001518 0.49661 23.5556
162 5Y3N 8MF 0.0008671 0.46258 23.5556
163 1TID ATP 0.0001673 0.50877 24.2647
164 3A0T ADP 0.003789 0.44236 32.8947
165 1QZR CDX 0.000329 0.54796 40
166 1QZR ANP 0.00007656 0.54133 40
167 1ZXM ANP 0.000007849 0.41672 43.1111
Pocket No.: 2; Query (leader) PDB : 4URN; Ligand: NOV; Similar sites found: 51
This union binding pocket(no: 2) in the query (biounit: 4urn.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3QDC RET 0.01591 0.40578 1.77778
2 4JJF FE9 0.04432 0.40055 2.22222
3 4IBF 1D5 0.02158 0.40057 2.32558
4 2QZX IVA VAL VAL STA ALA STA 0.008762 0.43139 2.33918
5 5CFT APC 0.02917 0.40174 2.7027
6 5CFT 51G 0.03342 0.40174 2.7027
7 2ZWA SAH 0.01878 0.41225 3.11111
8 4ZBR DIF 0.03668 0.40824 3.11111
9 4ZBR NPS 0.03504 0.40824 3.11111
10 1RYI FAD 0.04737 0.41012 3.55556
11 4OIV XX9 0.04897 0.40889 3.55556
12 1FCH TYR GLN SER LYS LEU 0.02185 0.40653 4
13 5BNW 12V 0.04941 0.40365 4
14 3S7O LBV 0.04839 0.40282 4.37318
15 1RJD SAM 0.01042 0.42469 4.44444
16 3VRV YSD 0.03778 0.42118 4.44444
17 5LGA 6VH 0.0314 0.41525 4.44444
18 3MMR ABH 0.02209 0.40033 4.44444
19 1LW4 TLP 0.01536 0.41256 4.88889
20 3V49 PK0 0.0316 0.40443 4.88889
21 5L7G 6QE 0.03167 0.40293 4.88889
22 2A3I C0R 0.03087 0.40203 4.88889
23 4I4B 1CV 0.03982 0.40934 5.33333
24 2NP9 YE1 0.03936 0.40761 5.33333
25 5K7H IVC 0.03092 0.40194 5.33333
26 3V1V GST 0.0199 0.40698 5.77778
27 2HHP FLC 0.00001788 0.40346 5.77778
28 5N8V KZZ 0.01585 0.40035 5.7971
29 2J9D ADP 0.02073 0.40896 5.88235
30 4ZOM 4Q3 0.02956 0.42122 6.22222
31 3SP6 IL2 0.02741 0.40145 6.22222
32 3OV6 MK0 0.04022 0.40609 6.66667
33 4V3I ASP LEU THR ARG PRO 0.007483 0.40163 6.66667
34 3P0K FAD 0.02344 0.40929 7.11111
35 4JZX 476 0.02342 0.40085 7.11111
36 3FAL REA 0.01777 0.40599 8.44444
37 1FM9 9CR 0.02869 0.4025 8.44444
38 4XB4 45D 0.03284 0.40042 8.55263
39 4QVX 3CQ 0.03014 0.4026 8.98204
40 4X6F 3XU 0.01774 0.43216 9.52381
41 4L2I NAD 0.01986 0.43625 9.77778
42 4L2I FAD 0.01406 0.43625 9.77778
43 3QFJ LEU LEU PHE GLY PHE PRO VAL TYR VAL 0.03215 0.42359 10
44 5C9J STE 0.01623 0.41179 10.101
45 5HGZ ACO 0.001972 0.469 10.2222
46 5KBZ 3B2 0.009423 0.44372 10.2222
47 1XVB 3BR 0.01827 0.40039 12.8889
48 5G5W R8C 0.03187 0.40748 13.7778
49 4P6X HCY 0.02472 0.40315 13.7778
50 3BQD DAY 0.03044 0.40013 13.7778
51 3ZOK NAD 0.03726 0.40842 14.2222
Pocket No.: 3; Query (leader) PDB : 4URN; Ligand: NOV; Similar sites found: 10
This union binding pocket(no: 3) in the query (biounit: 4urn.bio3) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3FSM 2NC 0.0417 0.40342 2.46305
2 3EMY IVA VAL VAL STA ALA STA 0.005903 0.4276 3.11111
3 5XDT GDP 0.01412 0.41981 3.11111
4 5XDT MB3 0.01956 0.41981 3.11111
5 4ZUL UN1 0.01691 0.41963 4.44444
6 4MNS 2AX 0.0237 0.42739 5.77778
7 5I39 FAD 0.02241 0.42179 5.77778
8 3Q9T FAY 0.04457 0.40571 5.77778
9 1LTH NAD 0.02531 0.40804 7.55556
10 4WJT NAG 0.01782 0.4019 9.58084
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