Receptor
PDB id Resolution Class Description Source Keywords
4HYM 1.9 Å EC: 5.99.1.3 PYRROLOPYRIMIDINE INHIBITORS OF DNA GYRASE B AND TOPOISOMERA PART I: STRUCTURE GUIDED DISCOVERY AND OPTIMIZATION OF DUALA GENTS WITH POTENT, BROAD-SPECTRUM ENZYMATIC ACTIVITY. FRANCISELLA TULARENSIS SUBSP. HOLARCTIORGANISM_TAXID: 376619 ATP-BINDING NUCLEOTIDE-BINDING TOPOISOMERASE ATP-BINDING ISOMERASE-ISOMERASE INHIBITOR COMPLEX
Ref.: PYRROLOPYRIMIDINE INHIBITORS OF DNA GYRASE B (GYRB) TOPOISOMERASE IV (PARE). PART I: STRUCTURE GUIDED D AND OPTIMIZATION OF DUAL TARGETING AGENTS WITH POTE BROAD-SPECTRUM ENZYMATIC ACTIVITY. BIOORG.MED.CHEM.LETT. V. 23 1529 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CJC A:401;
Valid;
none;
Ki = 6 nM
442.925 C19 H19 Cl N8 O S CCc1c...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4HY1 1.9 Å EC: 5.99.1.3 PYRROLOPYRIMIDINE INHIBITORS OF DNA GYRASE B AND TOPOISOMERA PART I: STRUCTURE GUIDED DISCOVERY AND OPTIMIZATION OF DUALA GENTS WITH POTENT, BROAD-SPECTRUM ENZYMATIC ACTIVITY. FRANCISELLA TULARENSIS SUBSP. HOLARCTIORGANISM_TAXID: 376619 ATP-BINDING NUCLEOTIDE-BINDING TOPOISOMERASE ATP-BINDING ISOMERASE-ISOMERASE INHIBITOR COMPLEX
Ref.: PYRROLOPYRIMIDINE INHIBITORS OF DNA GYRASE B (GYRB) TOPOISOMERASE IV (PARE). PART I: STRUCTURE GUIDED D AND OPTIMIZATION OF DUAL TARGETING AGENTS WITH POTE BROAD-SPECTRUM ENZYMATIC ACTIVITY. BIOORG.MED.CHEM.LETT. V. 23 1529 2013
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 4HY1 Ki = 2 nM 19X C20 H19 Cl N6 O S CCc1c(c2c(....
2 4HYM Ki = 6 nM CJC C19 H19 Cl N8 O S CCc1c(c2c(....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 4HY1 Ki = 2 nM 19X C20 H19 Cl N6 O S CCc1c(c2c(....
2 4HYM Ki = 6 nM CJC C19 H19 Cl N8 O S CCc1c(c2c(....
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: CJC; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 CJC 1 1
2 1A0 0.598131 0.873239
3 19X 0.5625 0.985915
4 SUY 0.436364 0.833333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4HY1; Ligand: 19X; Similar sites found: 58
This union binding pocket(no: 1) in the query (biounit: 4hy1.bio2) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1RYD GLC 0.004853 0.43398 1.55039
2 4IVG ANP 0.001228 0.45841 1.79487
3 5HSA FAS 0.02686 0.41287 2.05128
4 4ER2 IVA VAL VAL STA ALA STA 0.03059 0.40725 2.12121
5 1IZE IVA VAL VAL STA ALA STA 0.01062 0.41335 2.47678
6 3ZL8 ADP 0.003851 0.42925 2.5641
7 4GCZ ADP 0.003197 0.42906 2.5974
8 5DCH 1YO 0.01365 0.40759 2.60417
9 2O1V ADP 0.0000479 0.4978 2.82051
10 1I7M PUT 0.01849 0.40535 2.99625
11 2PYW SR1 0.01148 0.41184 3.07692
12 4XCL AGS 0.00003475 0.52593 3.0888
13 2C2A ADP 0.00005454 0.5117 3.10078
14 2VDF OCT 0.003022 0.41416 3.16206
15 2WGV CIT 0.01383 0.40809 3.22581
16 2ZKJ ADP 0.0001241 0.52853 3.33333
17 3GYT DL4 0.01359 0.40817 3.33333
18 1QY8 RDI 0.00000854 0.5464 3.34572
19 1GKZ ADP 0.0000735 0.50816 3.35052
20 1B8O IMH 0.01815 0.405 3.52113
21 1RL4 BRR 0.009268 0.41426 3.7234
22 3LVW GSH 0.03478 0.4015 3.84615
23 1VGR COA 0.02299 0.40741 4.10256
24 3IHB GLU 0.008093 0.41489 4.61538
25 2GFD RDA 0.00001293 0.55337 4.66102
26 3W8X FAD 0.03584 0.40886 5.38462
27 1BGQ RDC 0.00001758 0.5532 5.77778
28 1ID0 ANP 0.001488 0.43746 5.92105
29 5IDM ANP 0.00002704 0.52594 6.70391
30 4L2I NAD 0.02948 0.4133 6.93642
31 4L2I FAD 0.02038 0.4133 6.93642
32 5L2J 6UL 0.04016 0.41713 7.14286
33 5L2J 70E 0.04391 0.41617 7.14286
34 3EHG ATP 0.007408 0.40548 7.8125
35 5IXH OTP 0.02186 0.41749 8.07453
36 1EX7 5GP 0.01528 0.40343 8.60215
37 1YC4 43P 0.000003611 0.5572 9.4697
38 5EW9 5VC 0.01885 0.44946 9.5941
39 3NMQ 7PP 0.0009611 0.43723 10.4603
40 1Y8O ADP 0.00001969 0.51355 10.9375
41 3H4L ANP 0.00006583 0.51512 11.7166
42 5F5R ANP 0.00008925 0.47763 11.7949
43 1M48 FRG 0.001872 0.40961 12.0301
44 5Y3N 8MF 0.001812 0.43851 12.0513
45 3K60 ADP 0.0006068 0.43247 12.1076
46 5JXZ ISC 0.00977 0.40432 12.3077
47 5JXZ ISJ 0.00977 0.40432 12.3077
48 4B7P 9UN 0.000001914 0.62883 13.0435
49 3L9R L9R 0.03549 0.40204 13.2653
50 1I58 ADP 0.0001411 0.48716 14.2857
51 1I58 ACP 0.0005343 0.4719 14.2857
52 2IOR ADP 0.00006499 0.52108 14.4681
53 4BIX ADP 0.003527 0.40584 15.1007
54 3A0T ADP 0.001384 0.44823 18.4211
55 3D36 ADP 0.0004906 0.4694 19.5652
56 1TID ATP 0.0006718 0.46074 19.8529
57 1TH8 ADP 0.000452 0.45414 22.7586
58 2XCM ADP 0.00001826 0.51242 25
Pocket No.: 2; Query (leader) PDB : 4HY1; Ligand: 19X; Similar sites found: 18
This union binding pocket(no: 2) in the query (biounit: 4hy1.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5W4W 9WG 0.01462 0.4147 2.41692
2 5IXG OTP 0.04436 0.41089 3.5503
3 2O4N TPV 0.02957 0.40192 4.0404
4 4F07 FAD 0.02294 0.40165 4.21053
5 4C12 ADP 0.04386 0.41628 4.35897
6 3EHH ADP 0.01107 0.40093 4.58716
7 3ND6 ATP 0.03309 0.40665 4.67836
8 2Q7D ANP 0.02744 0.40359 4.91329
9 2XMY CDK 0.04511 0.42067 5.03356
10 4Q9N NAI 0.0397 0.40136 5.36913
11 2BTO GTP 0.0234 0.40575 7.40741
12 2Y91 98J 0.007505 0.41397 7.54717
13 2GJ5 VD3 0.02954 0.41343 8.02469
14 3GKJ HC3 0.02129 0.40163 8.62069
15 4ZUL UN1 0.01515 0.42213 9.74359
16 1Q1Y BB2 0.01542 0.401 12.5654
17 1N4H REA 0.02041 0.4058 14.6718
18 1GR0 NAD 0.04717 0.40055 20.436
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