Receptor
PDB id Resolution Class Description Source Keywords
4CKL 2.05 Å EC: 5.99.1.3 STRUCTURE OF 55 KDA N-TERMINAL DOMAIN OF E. COLI DNA GYRASE A SUBUNIT WITH SIMOCYCLINONE D8 BOUND ESCHERICHIA COLI ISOMERASE TOPOISOMERASE ANTIBIOTIC TARGET
Ref.: A NEW CRYSTAL STRUCTURE OF THE BIFUNCTIONAL ANTIBIO SIMOCYCLINONE D8 BOUND TO DNA GYRASE GIVES FRESH IN INTO THE MECHANISM OF INHIBITION. J.MOL.BIOL. V. 426 2023 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SM8 A:1522;
Valid;
none;
Kd = 44 nM
932.275 C46 H42 Cl N O18 C[C@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4CKL 2.05 Å EC: 5.99.1.3 STRUCTURE OF 55 KDA N-TERMINAL DOMAIN OF E. COLI DNA GYRASE A SUBUNIT WITH SIMOCYCLINONE D8 BOUND ESCHERICHIA COLI ISOMERASE TOPOISOMERASE ANTIBIOTIC TARGET
Ref.: A NEW CRYSTAL STRUCTURE OF THE BIFUNCTIONAL ANTIBIO SIMOCYCLINONE D8 BOUND TO DNA GYRASE GIVES FRESH IN INTO THE MECHANISM OF INHIBITION. J.MOL.BIOL. V. 426 2023 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 4CKL Kd = 44 nM SM8 C46 H42 Cl N O18 C[C@@H]1[C....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 4CKL Kd = 44 nM SM8 C46 H42 Cl N O18 C[C@@H]1[C....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4CKL Kd = 44 nM SM8 C46 H42 Cl N O18 C[C@@H]1[C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SM8; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 SM8 1 1
2 SMQ 0.761905 0.765625
3 7OX 0.757764 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4CKL; Ligand: SM8; Similar sites found: 141
This union binding pocket(no: 1) in the query (biounit: 4ckl.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2ZWS PLM 0.001278 0.50112 1.21704
2 4WBD CIT 0.0007919 0.48088 1.21704
3 1T10 F6P 0.006945 0.41665 1.21704
4 1AX2 NDG GAL 0.007178 0.41081 1.67364
5 1WDA BAG 0.002325 0.42583 1.82556
6 1A59 CIT 0.01169 0.41789 1.85185
7 4RPM HXC 0.04173 0.41696 1.97044
8 1I2B USQ 0.008436 0.43486 1.9802
9 1I2B NAD 0.008436 0.43486 1.9802
10 1I2B UPG 0.008436 0.43486 1.9802
11 4RJK PYR 0.008477 0.45563 2.0284
12 2VAR AMP 0.005876 0.40483 2.23642
13 1XX4 BAM 0.01528 0.4253 2.29885
14 2IZ1 ATR 0.01821 0.40343 2.32068
15 1RYI GOA 0.004112 0.47638 2.35602
16 2HFK E4H 0.007334 0.41042 2.50784
17 3TKA CTN 0.001231 0.51296 2.59366
18 3PLN U5P 0.00423 0.42045 2.59434
19 1PEA ACM 0.02123 0.41158 2.5974
20 3L6R MLI 0.01331 0.41525 2.60116
21 4B16 NAG 0.00004828 0.56476 2.63158
22 2Q8H TF4 0.001716 0.47332 2.7027
23 1FBL HTA 0.004439 0.40962 2.7027
24 2OWZ CIT 0.00656 0.42343 2.71084
25 2P69 PLP 0.002633 0.43493 2.94118
26 1KTC NGA 0.003036 0.42649 2.96296
27 1GPJ CIT 0.007293 0.42136 2.9703
28 1RYD GLC 0.00146 0.45274 3.10078
29 1XVV CCQ 0.006301 0.40001 3.18627
30 3NNF AKG 0.008657 0.418 3.19767
31 1Q0H FOM 0.004124 0.41234 3.20197
32 2ZJ5 ADP 0.007679 0.41476 3.24544
33 2QV7 ADP 0.002375 0.40661 3.2641
34 3F81 STT 0.01337 0.42825 3.27869
35 1DXY COI 0.03362 0.40783 3.3033
36 2Q37 3AL 0.001763 0.44248 3.31492
37 1YHM AHD 0.01193 0.40643 3.31492
38 4JLV ADP 0.0319 0.41954 3.34572
39 1JN2 SFP 0.006353 0.48361 3.37553
40 1NF8 BOG 0.004049 0.4394 3.38164
41 3PFG TLO 0.003321 0.41093 3.42205
42 3PFG SAM 0.003321 0.41093 3.42205
43 4CCO OGA 0.0108 0.40334 3.42612
44 1GJW GLC 0.001106 0.46564 3.44828
45 4O8A 2OP 0.002965 0.46133 3.44828
46 1KOL NAD 0.001297 0.42093 3.51759
47 2BZ1 TAU 0.005231 0.46725 3.57143
48 1JGS SAL 0.03247 0.4231 3.62319
49 4QVH FLC 0.04105 0.42027 3.65112
50 3OAI MAL 0.0315 0.40035 3.65112
51 4M51 BEZ 0.02754 0.40605 3.74707
52 1Y1A GSH 0.006762 0.4617 3.82514
53 3MAG 3MA 0.02835 0.41855 3.90879
54 1QDS PGA 0.003144 0.41552 3.98406
55 2Q3M MLA 0.0101 0.43443 3.98773
56 2JBH 5GP 0.004075 0.41594 4
57 4C2G ALA ALA ALA ALA 0.007154 0.40601 4.03587
58 4O1M NAD 0.003115 0.40014 4.12698
59 4PLG NAI 0.002597 0.4115 4.19162
60 4PLG OXM 0.002597 0.4115 4.19162
61 4BMO FMN 0.001051 0.41 4.20168
62 3NHB ADP 0.03005 0.40188 4.24837
63 1B8U OAA 0.002225 0.4078 4.25532
64 2B7N NTM 0.009303 0.41113 4.3956
65 3O2K QRP 0.001888 0.42423 4.43038
66 2F2U M77 0.001708 0.42594 4.47761
67 1SC3 MLI 0.008615 0.43066 4.49438
68 2NCD ADP 0.001221 0.4494 4.52381
69 1Q3P GLU ALA GLN THR ARG LEU 0.001892 0.42946 4.58716
70 3ZPG 5GP 0.02826 0.41169 4.71204
71 2DVZ GLU 0.001654 0.42649 4.77707
72 3UEC ALA ARG TPO LYS 0.01284 0.41598 4.79452
73 1O9U ADZ 0.01014 0.43435 4.85714
74 4M5P MLA 0.01767 0.42949 4.914
75 4M5P 23W 0.02113 0.41168 4.914
76 3BY8 MLT 0.0232 0.40393 4.92958
77 3SHR CMP 0.003381 0.41428 5.01672
78 1B74 DGN 0.02926 0.40476 5.11811
79 1QRD DQN 0.02592 0.40733 5.12821
80 3RF4 FUN 0.007138 0.41091 5.17241
81 2EB5 OXL 0.008455 0.41847 5.24345
82 3RFV 15L 0.001387 0.4076 5.24345
83 3BHO B4P 0.01612 0.43161 5.28846
84 2E1A MSE 0.007284 0.40569 5.33333
85 4JCA CIT 0.02407 0.42235 5.38922
86 4JP3 CIT 0.003489 0.4091 5.43933
87 3QDT A2G GAL 0.007968 0.43231 5.59441
88 3QDY A2G GAL 0.02501 0.4081 5.59441
89 3QDY CBS 0.02504 0.40237 5.59441
90 4K30 NLG 0.004891 0.40797 5.625
91 3P3N AKG 0.004174 0.43225 5.73066
92 1H2M OGA 0.003575 0.43528 5.76923
93 1PTR PRB 0.01564 0.41197 6
94 2XDQ MGX 0.007599 0.44068 6.30435
95 3KJQ B94 0.001106 0.42814 6.31579
96 3RK0 AMP 0.002044 0.41797 6.32911
97 1DL7 NCH 0.02943 0.4255 6.42202
98 3WUD GLC GAL 0.02532 0.40784 6.61765
99 3SCH TB6 0.005964 0.42529 7.07071
100 1H2K OGA 0.00602 0.4251 7.31707
101 1D6H COA 0.004155 0.41038 7.49354
102 1SS4 CIT 0.004101 0.46618 7.84314
103 1SS4 GSH 0.01167 0.45059 7.84314
104 1H8P PC 0.004799 0.45077 8.25688
105 1OAA OAA 0.006029 0.40455 8.49421
106 3SQG COM 0.002801 0.47181 8.60215
107 1C1L GAL BGC 0.003965 0.43982 8.75912
108 4F8L GAL 0.02561 0.42888 8.96552
109 1WRA PC 0.004153 0.43889 9.09091
110 1NU4 MLA 0.008047 0.40393 9.27835
111 2BO4 FLC 0.004199 0.43866 9.3199
112 3FW3 GLC 0.01558 0.45571 9.3985
113 2VQ5 LDP 0.02965 0.41063 9.45274
114 2VQ5 HBA 0.0184 0.40866 9.45274
115 1NML CIT 0.001395 0.44065 9.5092
116 1G8S MET 0.01795 0.40371 9.56522
117 1ULE GLA GAL NAG 0.003741 0.44824 10
118 3R51 MMA 0.01919 0.42027 10
119 1EYQ NAR 0.00928 0.40141 10.3604
120 1T0S BML 0.002549 0.45631 10.4651
121 4F4S EFO 0.009082 0.40651 10.5263
122 4W6Z ETF 0.004703 0.45122 10.951
123 2Q1A 2KT 0.01327 0.40964 11.2628
124 1Y7P RIP 0.03633 0.40013 11.6592
125 3E6J DR2 0.01176 0.43487 11.7904
126 3S9K CIT 0.009098 0.45996 11.8644
127 2D37 FMN 0.002091 0.40164 11.9318
128 2O66 FLC 0.01392 0.40352 12.5926
129 4AF5 CIT 0.02145 0.40021 13.1579
130 1U3I GSH 0.002955 0.43276 13.2701
131 3SJ0 DXC 0.0093 0.42254 14.0845
132 3PNA CMP 0.008705 0.40254 16.2338
133 4Q3F TLA 0.01052 0.41418 17.9487
134 4G28 0W8 0.002337 0.42574 18.7919
135 2V5E SCR 0.002365 0.47569 18.8119
136 4NC7 I3C 0.02411 0.40314 20.202
137 2VKL MLT 0.0194 0.42734 21.1111
138 2YLD CMO 0.005256 0.42776 22.0472
139 1UO5 PIH 0.003634 0.47602 26.4706
140 1UO4 PIH 0.03426 0.41415 26.4706
141 1JAC AMG 0.02038 0.4262 35
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