Receptor
PDB id Resolution Class Description Source Keywords
4JR7 1.48 Å EC: 2.7.11.1 CRYSTAL STRUCTURE OF SCCK2 ALPHA IN COMPLEX WITH GMPPNP SACCHAROMYCES CEREVISIAE PROTEIN KINASE PROTEIN PHOSPHORYLATION TRANSFERASE
Ref.: THE MULTIPLE NUCLEOTIDE-DIVALENT CATION BINDING MOD SACCHAROMYCES CEREVISIAE CK2 ALPHA INDICATE A POSSI CO-SUBSTRATE HYDROLYSIS PRODUCT (ADP/GDP) RELEASE P ACTA CRYSTALLOGR.,SECT.D V. 70 501 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GNP A:401;
Valid;
none;
submit data
522.196 C10 H17 N6 O13 P3 c1nc2...
MG A:402;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4JR7 1.48 Å EC: 2.7.11.1 CRYSTAL STRUCTURE OF SCCK2 ALPHA IN COMPLEX WITH GMPPNP SACCHAROMYCES CEREVISIAE PROTEIN KINASE PROTEIN PHOSPHORYLATION TRANSFERASE
Ref.: THE MULTIPLE NUCLEOTIDE-DIVALENT CATION BINDING MOD SACCHAROMYCES CEREVISIAE CK2 ALPHA INDICATE A POSSI CO-SUBSTRATE HYDROLYSIS PRODUCT (ADP/GDP) RELEASE P ACTA CRYSTALLOGR.,SECT.D V. 70 501 2014
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 133 families.
1 4JR7 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
2 4JQE - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
3 4MWH - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 4LFI - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 101 families.
1 4JR7 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
2 4JQE - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
3 4MWH - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 4LFI - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
50% Homology Family (80)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 3PXQ Kd = 37 uM 2AN C16 H13 N O3 S c1ccc(cc1)....
2 2R3N ic50 = 70 nM SCZ C21 H19 N5 c1ccc(cc1)....
3 1H0V - UN4 C10 H12 N6 O2 c1[nH]c2c(....
4 4NJ3 Kd = 0.3 uM 2KD C27 H21 Cl N2 O6 COC(=O)[C@....
5 1JSV - U55 C10 H11 N5 O2 S c1cc(ccc1N....
6 1OIQ ic50 = 2.9 uM HDU C14 H13 N5 O Cc1c(n2ccc....
7 2W17 ic50 = 0.002 uM I19 C24 H30 F N7 O Cc1ncc(n1C....
8 2VTP ic50 = 0.003 uM LZ9 C17 H11 F3 N4 O2 c1cc(c(c(c....
9 1JVP ic50 = 1.6 uM LIG C15 H11 N3 c1ccc-2c(c....
10 1FVT - 106 C14 H11 Br N4 O3 S c1cc(ccc1N....
11 4KD1 - 1QK C21 H29 N6 O2 CCc1cnn2c1....
12 3LE6 ic50 = 0.035 uM 2BZ C17 H10 Cl N5 O2 Cc1c-2nc(c....
13 2VTI ic50 = 0.66 uM LZ3 C14 H12 N4 O3 S c1ccc2c(c1....
14 3LFS Ki = 2.5 uM A07 C17 H16 Cl N3 O CCCC(=O)Nc....
15 1PXI - CK1 C8 H5 Cl2 N3 S c1cnc(nc1c....
16 4LYN - 1YG C20 H23 N3 O2 S2 C[C@@H](c1....
17 1YKR ic50 = 0.56 uM 628 C20 H14 Cl2 N4 O3 S c1cc(c(c(c....
18 1PXN Ki = 0.07 uM CK6 C15 H15 N5 O S Cc1c(sc(n1....
19 2R3J ic50 = 10 nM SCJ C18 H14 Br N5 c1ccc(cc1)....
20 6Q3F - HEW C5 H5 Br N2 c1cnc(cc1B....
21 3IG7 ic50 = 9 nM EFP C18 H22 N4 O3 CC(=O)NC1C....
22 2VTS ic50 = 0.03 uM LZC C16 H23 N7 CC(C)Nc1cc....
23 1P2A ic50 = 12 nM 5BN C17 H15 F N4 O c1cc([nH]c....
24 2BHE ic50 = 1 uM BRY C16 H9 Br N2 O2 c1ccc2c(c1....
25 3UNK ic50 = 15 uM 0BY C17 H13 Cl N4 O2 c1ccc(c(c1....
26 2VTQ ic50 = 0.14 uM LZA C16 H17 F2 N5 O2 c1cc(c(c(c....
27 2C68 ic50 = 1.8 uM CT6 C18 H15 Br N5 c1cc(cc(c1....
28 3TIZ - 3TI C17 H13 N O2 c1ccc2c(c1....
29 3PXY ic50 = 5.9 uM JWS C10 H11 N5 O2 COc1ccc(c(....
30 2R3M ic50 = 10 nM SCX C19 H17 F2 N7 CCc1cnn2c1....
31 6HOT - CIY C10 H10 O3 COc1cc(ccc....
32 5ORJ - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
33 3MB6 ic50 = 100 nM 01I C16 H8 O6 c1cc2c(cc(....
34 5M4F - 7FC C16 H8 Cl2 O5 c1cc(ccc1C....
35 6A1C - 9NX C17 H15 Br N4 O2 S COc1cc(c(c....
36 6EHU - B5E C25 H24 F3 N3 CCc1ccccc1....
37 5CVH - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
38 3BQC ic50 ~ 2 uM EMO C15 H10 O5 Cc1cc2c(c(....
39 6L22 - E3U C16 H12 O6 c1cc(c(c2c....
40 5N9K Ki = 0.46 nM 8QK C20 H13 Cl2 N O4 COc1ccc(cc....
41 5OTQ - AUH C25 H27 N3 O CCc1ccccc1....
42 5CU2 - 54G C8 H8 O3 Cc1ccc(c(c....
43 5MO5 - 4IH C17 H21 Cl N2 O2 S CS(=O)(=O)....
44 5M4I - 7FC C16 H8 Cl2 O5 c1cc(ccc1C....
45 5MP8 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
46 6HOR - GJK C11 H12 O3 CC(=O)/C=C....
47 4UZH ic50 = 9800 nM JVE C15 H13 F N4 O c1ccc(c(c1....
48 6R49 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
49 6R4A - JRT C17 H17 N3 O c1ccc(cc1)....
50 5OS1 Kd = 494 uM A7H C10 H11 N O S CCOc1ccc2c....
51 2C6E - HPM C28 H31 N7 O4 COc1cc2c(c....
52 3H0Y ic50 = 0.006 uM 48B C23 H17 Cl F N5 O2 c1ccc(c(c1....
53 4B0G ic50 = 0.015 uM VEK C19 H21 Br N8 O Cc1cc(no1)....
54 4JBP ic50 = 41 nM YPH C34 H36 N6 O4 c1ccc(cc1)....
55 3H10 - 97B C30 H25 Cl F2 N6 O CN1CCN(CC1....
56 6VPM - MLA C3 H4 O4 C(C(=O)O)C....
57 5Y9M - NIO C6 H5 N O2 c1cc(cnc1)....
58 7A1B ic50 = 2.36 uM QXW C5 H2 Br2 N4 c1c2c(nc(c....
59 7A2H - QX2 C6 H2 Br3 N3 c1[nH]c2c(....
60 1M2P - HNA C14 H7 N O6 c1cc2c(c(c....
61 1LPU - BEN C7 H8 N2 [H]/N=C(c1....
62 2QC6 ic50 = 0.1 uM G12 C10 H6 Br2 O3 CC1=C(C(=O....
63 4ANM ic50 = 28 nM WUL C15 H14 Br N3 O3 c1cc2c(cc1....
64 1DAW - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
65 4RLK - E91 C21 H14 N2 O2 c1ccc2c(c1....
66 2OXD - K32 C7 H2 Br4 N2 O c12c(c(c(c....
67 1JKL - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
68 3F5G - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
69 5AUZ ic50 = 98 uM GEN C15 H10 O5 c1cc(ccc1C....
70 4FG9 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
71 5L2T - 6ZZ C23 H30 N8 O CN(C)C(=O)....
72 3GC0 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
73 3MFU - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
74 3C0H - AMP C10 H14 N5 O7 P c1nc(c2c(n....
75 3C0I - 3AM C10 H14 N5 O7 P c1nc(c2c(n....
76 3MFS - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
77 5OMY - 9YE C23 H25 N O3 CC(C)n1c2c....
78 2YAB - AMP C10 H14 N5 O7 P c1nc(c2c(n....
79 2YAA - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
80 4JR7 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GNP; Similar ligands found: 129
No: Ligand ECFP6 Tc MDL keys Tc
1 9GM 1 1
2 GNP 1 1
3 GDP 0.839506 0.973684
4 GP3 0.82716 0.948718
5 GTP 0.809524 0.973684
6 GNH 0.807229 0.986842
7 GCP 0.77907 0.948718
8 G1R 0.77907 0.961039
9 GSP 0.770115 0.925
10 5GP 0.756098 0.960526
11 G 0.756098 0.960526
12 G2R 0.747253 0.936709
13 GMV 0.747126 0.948718
14 GAV 0.714286 0.936709
15 GP2 0.712644 0.936709
16 G2P 0.711111 0.936709
17 Y9Z 0.708333 0.880952
18 GDD 0.690722 0.936709
19 GKE 0.690722 0.936709
20 GDC 0.690722 0.936709
21 G5P 0.686869 0.948718
22 GPG 0.684211 0.936709
23 GFB 0.683673 0.936709
24 GDR 0.683673 0.936709
25 GTG 0.683673 0.91358
26 GDP BEF 0.681319 0.911392
27 GKD 0.68 0.936709
28 JB2 0.68 0.936709
29 6CK 0.676768 0.91358
30 G3A 0.676768 0.948718
31 GTP MG 0.673913 0.935065
32 GDX 0.673267 0.948718
33 ALF 5GP 0.67033 0.86747
34 YGP 0.663265 0.879518
35 GPD 0.656863 0.902439
36 GDP AF3 0.645833 0.86747
37 GDP ALF 0.645833 0.86747
38 JB3 0.641509 0.925
39 DBG 0.640351 0.974359
40 G3D 0.638298 0.960526
41 G4P 0.625 0.960526
42 GMP 0.621951 0.857143
43 NGD 0.62037 0.936709
44 GGM 0.618182 0.925926
45 0O2 0.616162 0.960526
46 KB7 0.612903 0.807229
47 2MD 0.603604 0.870588
48 CAG 0.60177 0.904762
49 FEG 0.590909 0.858824
50 U2G 0.590909 0.91358
51 GDP 7MG 0.590476 0.888889
52 MGD 0.587719 0.870588
53 ZGP 0.585586 0.848837
54 CG2 0.580357 0.91358
55 KBD 0.568627 0.807229
56 ANP 0.568421 0.922078
57 PGD 0.567797 0.902439
58 MD1 0.567797 0.870588
59 3GP 0.56044 0.922078
60 TPG 0.558333 0.822222
61 GH3 0.55 0.948052
62 KBJ 0.54717 0.77907
63 FE9 0.546219 0.778947
64 GPX 0.539216 0.922078
65 G4M 0.539062 0.860465
66 DGI 0.536082 0.9
67 BGO 0.535088 0.901235
68 IDP 0.53125 0.947368
69 DGT 0.53 0.9
70 2GP 0.526882 0.935065
71 G1R G1R 0.520325 0.901235
72 QBQ 0.515152 0.960526
73 I2C FE2 CMO CMO 0.508197 0.811111
74 AGO 0.504202 0.91358
75 P2G 0.5 0.860759
76 G1G 0.5 0.902439
77 MGP 0.49505 0.936709
78 R5I 0.49505 0.922078
79 R7I 0.49505 0.922078
80 PGD O 0.492063 0.831461
81 6G0 0.490196 0.936709
82 P1G 0.489796 0.85
83 AKW 0.483051 0.869048
84 DG 0.474227 0.8875
85 DGP 0.474227 0.8875
86 IMP 0.463918 0.934211
87 G2Q 0.462963 0.936709
88 CZF 0.460784 0.909091
89 GPC 0.459677 0.858824
90 G C 0.459016 0.878049
91 GTA 0.448276 0.91358
92 G7M 0.444444 0.924051
93 MAP 0.439252 0.898734
94 B4P 0.434343 0.871795
95 ADP 0.434343 0.896104
96 AP5 0.434343 0.871795
97 A2D 0.43299 0.871795
98 AT4 0.43 0.8625
99 SGP 0.425743 0.807229
100 AU1 0.425743 0.922078
101 BA3 0.424242 0.871795
102 APC G U 0.423077 0.864198
103 C2E 0.423077 0.897436
104 35G 0.423077 0.909091
105 PCG 0.423077 0.909091
106 HEJ 0.421569 0.896104
107 ATP 0.421569 0.896104
108 ACQ 0.419048 0.873418
109 5GP 5GP 0.419048 0.860759
110 AQP 0.417476 0.896104
111 5FA 0.417476 0.896104
112 01G 0.417391 0.880952
113 UNP 0.415842 0.810127
114 AN2 0.415842 0.909091
115 6AD 0.415094 0.821429
116 M33 0.411765 0.860759
117 ITT 0.411765 0.846154
118 JSQ 0.409524 0.851852
119 HFD 0.409524 0.851852
120 ACP 0.407767 0.873418
121 KG4 0.407767 0.873418
122 6YZ 0.407407 0.873418
123 AR6 0.403846 0.871795
124 APR 0.403846 0.871795
125 A4P 0.403226 0.848837
126 UCG 0.402985 0.888889
127 M7G A2M G 0.4 0.791209
128 AD9 0.4 0.873418
129 AGS 0.4 0.851852
Similar Ligands (3D)
Ligand no: 1; Ligand: GNP; Similar ligands found: 41
No: Ligand Similarity coefficient
1 BEF GDP 0.9966
2 ALF GDP 0.9853
3 BEF ADP 0.9788
4 DTP 0.9719
5 ADP BEF 0.9564
6 ADP ALF 0.9518
7 GDP MG 0.9489
8 ADP AF3 0.9407
9 UTP 0.9203
10 ADP MG 0.9170
11 CTP 0.9164
12 ATF 0.9160
13 MGT 0.9145
14 P5A 0.9069
15 APC 0.8983
16 AMO 0.8940
17 DSZ 0.8934
18 SSA 0.8828
19 TSB 0.8826
20 A12 0.8814
21 ATP MG 0.8808
22 8X1 0.8806
23 PR8 0.8796
24 DAT 0.8750
25 5AL 0.8746
26 MGO 0.8726
27 NSS 0.8721
28 G5A 0.8710
29 3AT 0.8675
30 SRP 0.8665
31 SAM 0.8658
32 TAT 0.8655
33 A5A 0.8651
34 4AD 0.8639
35 KAA 0.8631
36 8DG 0.8607
37 VO4 ADP 0.8602
38 GCP G 0.8590
39 ADX 0.8588
40 ANP MG 0.8566
41 TTP 0.8526
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4JR7; Ligand: GNP; Similar sites found with APoc: 29
This union binding pocket(no: 1) in the query (biounit: 4jr7.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 6LVK EVC 21.0863
2 3SRV S19 21.6607
3 3IOK 1P6 21.7252
4 3E8N ATP 23.1672
5 3E8N VRA 23.1672
6 4WB7 ATP 23.5294
7 6YNC 7CT 24.9292
8 2QCS ANP 25.1429
9 5IZF 6J9 AZ1 DAR ACA DAR NH2 25.9259
10 4WB6 ATP 26.2857
11 3LXN MI1 27.9874
12 1XJD STU 28.0749
13 4N70 2HX 28.3422
14 6OVA N9G 29.9003
15 4FG8 ATP 30.4762
16 2JLD AG1 31.016
17 2JLD AG1 31.016
18 5WO4 B7V 31.1258
19 4UX9 ANP 33.7912
20 4UX9 ANP 33.7912
21 2VZ6 FEF 34.1853
22 1PHK ATP 35.2349
23 2VN9 GVD 36.5448
24 2VN9 GVD 36.5448
25 3RWP ABQ 37.7005
26 3RWP ABQ 37.7005
27 4NST AF3 40.9091
28 2XMY CDK 44.6309
29 5HQ0 LZ9 45.0331
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