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Receptor
PDB id Resolution Class Description Source Keywords
4GFD 1.8 Å EC: 2.7.4.9 THYMIDYLATE KINASE (TMK) FROM S. AUREUS IN COMPLEX WITH TK-6 STAPHYLOCOCCUS AUREUS SUBSP. AUREUS KINASE THYMIDINE MONPHOSPHATE SOLUBLE TRANSFERASE-TRANSFEINHIBITOR COMPLEX
Ref.: IN VIVO VALIDATION OF THYMIDYLATE KINASE (TMK) WITH RATIONALLY DESIGNED, SELECTIVE ANTIBACTERIAL COMPOU ACS CHEM.BIOL. V. 7 1866 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
0YB A:301;
B:301;
Valid;
Valid;
none;
none;
Ki = 330 pM
584.501 C29 H34 Br N3 O5 CC1=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4GFD 1.8 Å EC: 2.7.4.9 THYMIDYLATE KINASE (TMK) FROM S. AUREUS IN COMPLEX WITH TK-6 STAPHYLOCOCCUS AUREUS SUBSP. AUREUS KINASE THYMIDINE MONPHOSPHATE SOLUBLE TRANSFERASE-TRANSFEINHIBITOR COMPLEX
Ref.: IN VIVO VALIDATION OF THYMIDYLATE KINASE (TMK) WITH RATIONALLY DESIGNED, SELECTIVE ANTIBACTERIAL COMPOU ACS CHEM.BIOL. V. 7 1866 2012
Members (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 4QGA ic50 = 12 nM 31Z C24 H23 Cl F N3 O5 CC1=CN(C(=....
2 4HLD ic50 = 0.5 nM 16T C22 H22 Cl N3 O6 S CC1=CN(C(=....
3 4QGG ic50 = 1 nM 32C C28 H31 Cl F N3 O5 CC1=CN(C(=....
4 4QGF ic50 = 69 nM 32B C27 H30 Cl N3 O6 CC[C@H](c1....
5 4QG7 ic50 = 10 nM 32K C25 H26 Cl N3 O6 CC1=CN(C(=....
6 4QGH ic50 = 1 nM 32E C28 H31 Cl F N3 O5 CC1=CN(C(=....
7 4GFD Ki = 330 pM 0YB C29 H34 Br N3 O5 CC1=CN(C(=....
8 2CCJ - TMP C10 H15 N2 O8 P CC1=CN(C(=....
9 2CCG - TMP C10 H15 N2 O8 P CC1=CN(C(=....
10 4HDC ic50 = 1.2 nM 13Y C28 H32 Cl N3 O5 CC1=CN(C(=....
11 4HEJ ic50 = 24000 nM 14D C24 H24 F3 N3 O3 CC1=CN(C(=....
12 4GSY ic50 = 120 nM 0Y5 C25 H24 F3 N3 O5 CC1=CN(C(=....
13 4HLC ic50 = 174 nM T05 C24 H25 N3 O7 S Cc1cccc(c1....
70% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 4QGA ic50 = 12 nM 31Z C24 H23 Cl F N3 O5 CC1=CN(C(=....
2 4HLD ic50 = 0.5 nM 16T C22 H22 Cl N3 O6 S CC1=CN(C(=....
3 4QGG ic50 = 1 nM 32C C28 H31 Cl F N3 O5 CC1=CN(C(=....
4 4QGF ic50 = 69 nM 32B C27 H30 Cl N3 O6 CC[C@H](c1....
5 4QG7 ic50 = 10 nM 32K C25 H26 Cl N3 O6 CC1=CN(C(=....
6 4QGH ic50 = 1 nM 32E C28 H31 Cl F N3 O5 CC1=CN(C(=....
7 4GFD Ki = 330 pM 0YB C29 H34 Br N3 O5 CC1=CN(C(=....
8 2CCJ - TMP C10 H15 N2 O8 P CC1=CN(C(=....
9 2CCG - TMP C10 H15 N2 O8 P CC1=CN(C(=....
10 4HDC ic50 = 1.2 nM 13Y C28 H32 Cl N3 O5 CC1=CN(C(=....
11 4HEJ ic50 = 24000 nM 14D C24 H24 F3 N3 O3 CC1=CN(C(=....
12 4GSY ic50 = 120 nM 0Y5 C25 H24 F3 N3 O5 CC1=CN(C(=....
13 4HLC ic50 = 174 nM T05 C24 H25 N3 O7 S Cc1cccc(c1....
50% Homology Family (54)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2YOH Ki = 11 uM WMJ C17 H19 N5 O7 CC1=CN(C(=....
2 2YOF Ki = 25 uM 74W C18 H18 Cl F3 N4 O4 S CC1=CN(C(=....
3 2WWF - TMP C10 H15 N2 O8 P CC1=CN(C(=....
4 2YOG Ki = 31 uM 74X C18 H18 Cl F3 N4 O4 S CC1=CN(C(=....
5 2V54 - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
6 4QGF ic50 = 69 nM 32B C27 H30 Cl N3 O6 CC[C@H](c1....
7 4QG7 ic50 = 10 nM 32K C25 H26 Cl N3 O6 CC1=CN(C(=....
8 4QGH ic50 = 1 nM 32E C28 H31 Cl F N3 O5 CC1=CN(C(=....
9 4GFD Ki = 330 pM 0YB C29 H34 Br N3 O5 CC1=CN(C(=....
10 2CCJ - TMP C10 H15 N2 O8 P CC1=CN(C(=....
11 2CCG - TMP C10 H15 N2 O8 P CC1=CN(C(=....
12 4HDC ic50 = 1.2 nM 13Y C28 H32 Cl N3 O5 CC1=CN(C(=....
13 4HEJ ic50 = 24000 nM 14D C24 H24 F3 N3 O3 CC1=CN(C(=....
14 4GSY ic50 = 120 nM 0Y5 C25 H24 F3 N3 O5 CC1=CN(C(=....
15 4HLC ic50 = 174 nM T05 C24 H25 N3 O7 S Cc1cccc(c1....
16 4TMK Kd = 20 nM T5A C20 H30 N7 O23 P5 CC1=CN(C(=....
17 1E2Q - TMP C10 H15 N2 O8 P CC1=CN(C(=....
18 1E9C - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
19 1NN0 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
20 1E2G - TMP C10 H15 N2 O8 P CC1=CN(C(=....
21 1NN1 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
22 1NMX - FDM C10 H14 F N2 O7 P CC1=CN(C(=....
23 1E2E - AF3 Al F3 F[Al](F)F
24 1NN5 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
25 1E9B - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
26 1E2D - TMP C10 H15 N2 O8 P CC1=CN(C(=....
27 1E99 - ATM C10 H14 N5 O7 P CC1=CN(C(=....
28 1NMY - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
29 2XX3 - TAE C9 H14 N2 O8 P2 CC1=CN(C(=....
30 1NMZ - NYM C10 H16 N3 O7 P CC1=CN(C(=....
31 1E9D - ATM C10 H14 N5 O7 P CC1=CN(C(=....
32 1NN3 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
33 1E9A - Z5A C20 H24 N10 O22 P5 CC1=CN(C(=....
34 1E9F - TMP C10 H15 N2 O8 P CC1=CN(C(=....
35 1E9E - TMP C10 H15 N2 O8 P CC1=CN(C(=....
36 1E98 - ATM C10 H14 N5 O7 P CC1=CN(C(=....
37 1E2F - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
38 2TMK - ATM C10 H14 N5 O7 P CC1=CN(C(=....
39 3TMK Kd = 135 nM T5A C20 H30 N7 O23 P5 CC1=CN(C(=....
40 1TMK - TMP C10 H15 N2 O8 P CC1=CN(C(=....
41 5X8C - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
42 5ZB4 - TMP C10 H15 N2 O8 P CC1=CN(C(=....
43 5ZAX - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
44 5X86 - TMP C10 H15 N2 O8 P CC1=CN(C(=....
45 5X8B - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
46 3UWO ic50 = 20 uM 0DJ C14 H12 N4 O2 CN1c2cc(cn....
47 3UXM ic50 = 17 uM 0DN C10 H13 F N2 O4 CC1=CN(C(=....
48 5UIV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
49 5XB2 - TMP C10 H15 N2 O8 P CC1=CN(C(=....
50 5XB3 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
51 5XAI - TMP C10 H15 N2 O8 P CC1=CN(C(=....
52 5H56 - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
53 5H5B - FLC C6 H5 O7 C(C(=O)[O-....
54 5H5K - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 0YB; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 0YB 1 1
2 13Y 0.666667 0.934211
3 32B 0.531746 0.8625
4 32C 0.519685 0.922078
5 32E 0.519685 0.922078
6 0Y5 0.484127 0.894737
7 T05 0.468254 0.725275
8 31Z 0.427481 0.883117
9 32K 0.427481 0.873418
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4GFD; Ligand: 0YB; Similar sites found with APoc: 157
This union binding pocket(no: 1) in the query (biounit: 4gfd.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 4V1F BQ1 None
2 5MWE TCE None
3 5UGW GSH None
4 5TVI O8N None
5 5NNT DPV None
6 3KPE TM3 None
7 1HBK MYR None
8 5N8V KZZ None
9 3NFD COA None
10 4LWU 20U None
11 4F4S EFO None
12 5XQL C2E 1.46341
13 5L7G LYS SER LEU LEU GLN GLN LEU LEU THR GLU 1.46341
14 5ZKC 3C0 1.95122
15 1XX4 BAM 1.95122
16 5M37 9SZ 1.95122
17 5M36 9SZ 1.95122
18 5XJ7 87O 1.99005
19 1M48 FRG 2.25564
20 4K55 H6P 2.41935
21 1JAY F42 2.43902
22 5LWY OLB 2.43902
23 2YFB SIN 2.43902
24 5LWY OLA 2.43902
25 5W3Y IHP 2.43902
26 6GN6 MAL 2.43902
27 1NQ7 HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU 2.43902
28 4O4Z N2O 2.5974
29 5VRH OLB 2.92683
30 1PIG GLC GLC 2.92683
31 6FP4 E1T 2.92683
32 6FP4 FAD 2.92683
33 2RH1 CLR 2.92683
34 3AQT RCO 2.92683
35 5EK3 5PK 2.92683
36 4TQ3 GPP 2.92683
37 4WGF HX2 2.92683
38 4NZF ARB 2.92683
39 2WOR 2AN 3
40 1RL4 BL5 3.19149
41 1NF8 BOG 3.41463
42 1E4I NFG 3.41463
43 2BHW NEX 3.41463
44 4RW3 SHV 3.41463
45 4RW3 PLM 3.41463
46 3W54 RNB 3.41463
47 4Q0A GLY HIS LYS ILE LEU HIS ARG LEU LEU GLN 3.41463
48 4Q0A 4OA 3.41463
49 1P72 THM 3.41463
50 3HYW DCQ 3.41463
51 5IKR ID8 3.41463
52 2GWH PCI 3.90244
53 3X01 AMP 3.90244
54 4G8R 96P 3.90244
55 4V3I ASP LEU THR ARG PRO 3.90244
56 5E70 RCD 3.90244
57 2JFZ 003 3.90244
58 2JFZ DGL 3.90244
59 4XCP PLM 4.11765
60 4HBM 0Y7 4.16667
61 4LSJ LSJ 4.39024
62 2BCG GER 4.39024
63 1M2Z BOG 4.39024
64 4KTP BGC 4.39024
65 4IA6 EIC 4.39024
66 2OZ5 7XY 4.39024
67 5OSW DIU 4.39024
68 6CB2 OLC 4.87805
69 4NRT 2NG 4.87805
70 1SGJ OAA 4.87805
71 1V6A TRE 4.87805
72 1N13 AG2 5.30973
73 3NB0 G6P 5.36585
74 1ND4 KAN 5.36585
75 4MRP GSH 5.36585
76 4MZU TDR 5.36585
77 2XN5 FUN 5.36585
78 1TV5 N8E 5.36585
79 2GEK GDP 5.36585
80 1XMY ROL 5.36585
81 3R9V DXC 5.36585
82 5V4R MGT 5.55556
83 5C1M OLC 5.6
84 3TDC 0EU 5.85366
85 6BMS POV 5.85366
86 1RV1 IMZ 5.88235
87 4URX FK1 5.94595
88 5FPN KYD 6.34146
89 4UCC ZKW 6.34146
90 6CS8 F9Y 6.34146
91 5E58 CPZ 6.34146
92 4UMJ BFQ 6.34146
93 4YSX E23 6.38298
94 5N26 CPT 6.59341
95 3KP6 SAL 6.62252
96 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 6.82927
97 3AI3 SOE 6.82927
98 3E70 GDP 6.82927
99 1VRP IOM 6.82927
100 6EVN PRO PRO GLY PRO ALA GLY PRO PRO GLY 6.86275
101 3AQA BYH 7.03125
102 5I8F ML1 7.27273
103 4URN NOV 7.31707
104 3WIR BGC 7.31707
105 2JC9 ADN 7.31707
106 5LX9 OLB 7.31707
107 5LX9 OLA 7.31707
108 3NJQ NJQ 7.77202
109 3VM7 GLC 7.80488
110 2P4Y C03 7.80488
111 3FUR Z12 7.80488
112 4TV1 36M 8.29268
113 5IUY BOG 8.29268
114 6BR8 PGV 8.29268
115 4TUZ 36J 8.29268
116 6BR8 6OU 8.29268
117 1ZED PNP 8.29268
118 6BR9 6OU 8.78049
119 1GNI OLA 8.78049
120 3HP8 SUC 9.09091
121 4G86 BNT 9.26829
122 3G58 988 9.26829
123 2Q8G AZX 9.7561
124 1MID LAP 9.89011
125 5KD8 TNR 10.2439
126 1NU4 MLA 10.3093
127 6GMN F4E 10.3093
128 3I7V ATP 10.4478
129 5KOR GDP 10.7317
130 3KO0 TFP 10.8911
131 5CHR 4NC 10.9489
132 5A0U CHT 11.2195
133 2JHP GUN 11.2195
134 6CGN DA 11.2195
135 3SQP 3J8 11.7073
136 5LXT GDP 11.8881
137 2VWA PTY 12.8713
138 4OGQ 7PH 13.5135
139 3OGN 3OG 13.7097
140 2HHP FLC 14.1463
141 1R6N 434 14.1463
142 2Y69 CHD 14.2857
143 1RV0 NDG 14.375
144 2ALG DAO 15.2174
145 2GJ5 VD3 15.4321
146 5W7B MYR 15.6028
147 2HZL PYR 15.6098
148 3B6C SDN 17.0732
149 1Y4Z PCI 17.561
150 5OCA 9QZ 17.561
151 5Z84 CHD 19.1489
152 5ZCO CHD 19.1489
153 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 21.4634
154 5BVT PAM 23.8806
155 4Q1A 2XZ 33.6585
156 4Q1A UDP 33.6585
157 2JAQ DCP 37.561
Pocket No.: 2; Query (leader) PDB : 4GFD; Ligand: 0YB; Similar sites found with APoc: 18
This union binding pocket(no: 2) in the query (biounit: 4gfd.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 4AF5 CIT None
2 5TVI MYR None
3 4V2O CLQ None
4 3W5N RAM 2.92683
5 2RH1 CAU 2.92683
6 4B16 NAG 3.90244
7 4JWK CTN 4.14508
8 2HFK E4H 4.39024
9 1O9U ADZ 4.39024
10 1JX6 AI2 4.39024
11 5HCN DAO 4.87805
12 5NM7 GLY 5.36585
13 1T0S BML 5.85366
14 4M51 BEZ 6.82927
15 1OGX EQU 6.87023
16 3RMK BML 7.80488
17 1M6P M6P 12.5
18 5W97 CHD 19.1489
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