Receptor
PDB id Resolution Class Description Source Keywords
4F9C 2.08 Å EC: 2.7.11.1 HUMAN CDC7 KINASE IN COMPLEX WITH DBF4 AND XL413 HOMO SAPIENS SER/THR PROTEIN KINASE TRANSFERASE PHOSPHORYLATION CELL CCELL DIVISION MITOSIS S PHASE SERINE/THREONINE-PROTEIN KDBF4-DEPENDENT KINASE DDK ATP-BINDING NUCLEOTIDE-BINDINGBINDING NUCLEUS TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: CRYSTAL STRUCTURE OF HUMAN CDC7 KINASE IN COMPLEX W ACTIVATOR DBF4. NAT.STRUCT.MOL.BIOL. V. 19 1101 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
0SX A:601;
Valid;
none;
submit data
289.717 C14 H12 Cl N3 O2 c1cc2...
ZN B:401;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6YA6 1.44 Å EC: 2.7.11.1 MINIMAL CONSTRUCT OF CDC7-DBF4 BOUND TO XL413 HOMO SAPIENS KINASE CDC7 DBF4 CELL CYCLE BIVALENT SUBSTRATE TRANSFER
Ref.: STRUCTURAL BASIS FOR THE ACTIVATION AND TARGET SITE SPECIFICITY OF CDC7 KINASE. STRUCTURE V. 28 954 2020
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 133 families.
1 6YA6 - 0SX C14 H12 Cl N3 O2 c1cc2c(cc1....
2 4F99 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 4F9C - 0SX C14 H12 Cl N3 O2 c1cc2c(cc1....
4 4F9B - 0SY C12 H11 N3 O c1cnccc1c2....
5 4F9A - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
6 6YA8 - ADP BEF n/a n/a
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 101 families.
1 6YA6 - 0SX C14 H12 Cl N3 O2 c1cc2c(cc1....
2 4F99 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 4F9C - 0SX C14 H12 Cl N3 O2 c1cc2c(cc1....
4 4F9B - 0SY C12 H11 N3 O c1cnccc1c2....
5 4F9A - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
6 6YA8 - ADP BEF n/a n/a
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 70 families.
1 6YA6 - 0SX C14 H12 Cl N3 O2 c1cc2c(cc1....
2 4F99 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 4F9C - 0SX C14 H12 Cl N3 O2 c1cc2c(cc1....
4 4F9B - 0SY C12 H11 N3 O c1cnccc1c2....
5 4F9A - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
6 6YA8 - ADP BEF n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 0SX; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 0SX 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: 0SX; Similar ligands found: 222
No: Ligand Similarity coefficient
1 2LW 0.9361
2 SU9 0.9336
3 22T 0.9297
4 74Z 0.9238
5 KMP 0.9176
6 BHF 0.9173
7 5KN 0.9162
8 34L 0.9137
9 D80 0.9080
10 6XC 0.9065
11 HWB 0.9056
12 FX5 0.9056
13 WUL 0.9050
14 69W 0.9044
15 PZB 0.9040
16 KXN 0.9032
17 FSE 0.9024
18 LI7 0.9006
19 DX7 0.9006
20 ET0 0.9006
21 NIF 0.9005
22 K8W 0.8990
23 9XZ 0.8988
24 Q8D 0.8987
25 1CE 0.8982
26 4RV 0.8981
27 L07 0.8978
28 52F 0.8974
29 761 0.8970
30 EV2 0.8969
31 0MB 0.8966
32 LIG 0.8962
33 3XL 0.8959
34 1V4 0.8958
35 QUE 0.8955
36 JVD 0.8953
37 TCR 0.8952
38 YE7 0.8942
39 39Z 0.8937
40 CUE 0.8936
41 Q8G 0.8934
42 DQH 0.8934
43 U5P 0.8928
44 EY7 0.8920
45 IQZ 0.8920
46 BL6 0.8917
47 JTF 0.8915
48 6JO 0.8909
49 MRI 0.8907
50 D87 0.8902
51 ADL 0.8895
52 KU1 0.8894
53 DX2 0.8891
54 CC6 0.8890
55 YZ9 0.8885
56 HKK 0.8884
57 62D 0.8881
58 XG1 0.8880
59 GNJ 0.8880
60 8RK 0.8878
61 3WL 0.8878
62 ML2 0.8861
63 C09 0.8859
64 BRY 0.8856
65 0H5 0.8855
66 MYC 0.8853
67 1EL 0.8849
68 AXX 0.8841
69 49P 0.8841
70 JHY 0.8841
71 4HG 0.8838
72 S0J 0.8835
73 1V3 0.8834
74 18E 0.8833
75 E3U 0.8829
76 MYU 0.8828
77 EYM 0.8824
78 GNV 0.8816
79 P4L 0.8814
80 VKE 0.8809
81 UN9 0.8808
82 108 0.8799
83 F40 0.8798
84 UMP 0.8797
85 UN3 0.8796
86 4AU 0.8793
87 9KZ 0.8787
88 40N 0.8786
89 3QI 0.8786
90 DH2 0.8783
91 J8G 0.8780
92 AGI 0.8778
93 HC8 0.8775
94 1AJ 0.8772
95 4E2 0.8771
96 272 0.8770
97 K4T 0.8769
98 DDC 0.8765
99 27M 0.8764
100 2GQ 0.8762
101 3DE 0.8757
102 NAR 0.8756
103 1R5 0.8753
104 RKY 0.8751
105 SDN 0.8750
106 3AK 0.8750
107 X2L 0.8749
108 AZN 0.8749
109 0UL 0.8749
110 LU2 0.8747
111 6QT 0.8746
112 YE6 0.8744
113 6JM 0.8742
114 X2M 0.8740
115 AO 0.8738
116 OTA 0.8738
117 KM2 0.8737
118 A05 0.8737
119 FNT 0.8733
120 20D 0.8731
121 A0O 0.8731
122 A73 0.8728
123 DT7 0.8727
124 D25 0.8727
125 5WK 0.8727
126 A8D 0.8727
127 NPS 0.8725
128 EY2 0.8725
129 SNJ 0.8725
130 PIQ 0.8723
131 HY7 0.8722
132 517 0.8718
133 2PW 0.8717
134 OAL 0.8714
135 L1T 0.8714
136 0LA 0.8713
137 KWV 0.8713
138 AJ1 0.8710
139 CX4 0.8709
140 5SB 0.8707
141 GNY 0.8707
142 IQ5 0.8704
143 19E 0.8700
144 NRA 0.8699
145 0DF 0.8699
146 S62 0.8698
147 57D 0.8693
148 HA6 0.8692
149 OAQ 0.8692
150 9CE 0.8689
151 25F 0.8685
152 DFL 0.8684
153 CKA 0.8682
154 3JC 0.8680
155 1V1 0.8679
156 1Q4 0.8678
157 LP8 0.8672
158 P83 0.8669
159 JTA 0.8668
160 2UD 0.8667
161 AQN 0.8667
162 0OK 0.8661
163 IRH 0.8660
164 KCH 0.8658
165 3RH 0.8658
166 1XS 0.8657
167 FZ0 0.8657
168 4QX 0.8653
169 0LO 0.8653
170 RDT 0.8643
171 1FE 0.8642
172 DX8 0.8641
173 RF2 0.8640
174 II4 0.8639
175 ML1 0.8637
176 DFV 0.8634
177 OAI 0.8632
178 4R0 0.8630
179 BVD 0.8626
180 5EZ 0.8626
181 7G2 0.8625
182 RHN 0.8625
183 QR2 0.8623
184 WLH 0.8623
185 HH6 0.8621
186 JOB 0.8621
187 YEX 0.8620
188 OPA 0.8620
189 1HP 0.8620
190 NVS 0.8618
191 J1K 0.8616
192 BBP 0.8615
193 Q5M 0.8612
194 5B2 0.8612
195 V2Z 0.8606
196 6JJ 0.8603
197 LC1 0.8599
198 3F4 0.8598
199 HRM 0.8598
200 P34 0.8596
201 C5P 0.8592
202 5NN 0.8589
203 J38 0.8589
204 7LU 0.8586
205 U7E 0.8583
206 AX1 0.8583
207 AFT 0.8583
208 5DE 0.8583
209 HHB 0.8582
210 5E2 0.8580
211 2QU 0.8578
212 28S 0.8571
213 7EH 0.8568
214 LZJ 0.8566
215 M78 0.8565
216 SZ5 0.8563
217 79X 0.8556
218 TVC 0.8552
219 1OT 0.8551
220 8CC 0.8518
221 78P 0.8517
222 C4E 0.8517
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6YA6; Ligand: 0SX; Similar sites found with APoc: 8
This union binding pocket(no: 1) in the query (biounit: 6ya6.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 5WO4 B7V 21.5232
2 5WO4 B7V 21.5232
3 5LI1 ANP 25.7062
4 3TXO 07U 28.9308
5 4WB7 ATP 31.1978
6 2QCS ANP 31.4286
7 4WB6 ATP 32.5714
8 2XMY CDK 47.3154
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