Kinase expression constructs

Information

Background:

The aim is to select a panel of kinases suitable for E. coli expression in 96-well plates.
Ideally, the kinase catalytic domain is to be expressed in isolation.
Plasmids are provided from two libraries: Construct spans are provided from PDB entries with E. coli expression system annotations.

Custom selection procedure:

Description of table fields with details of selection procedure:

targetID Kinase domain targets are given an identifier consisting of UniProt entry name followed by the kinase domain index (since some kinases have two catalytic domains)
DB_target_rank Qualitative ranking of human kinase importance, based on metrics such as number of bioassays, number of PDBs, number of publications, % mutation rate in sequenced tumor samples
plasmid_ID For a given kinase target, all matching plasmids from the available plasmid libraries (see plasmid_source) are aligned and sorted based on nconflicts and nextraneous_residues (see below), and the top-ranked plasmid is selected (click the targetID to see the alignment)
plasmid_source Source of the top-ranked plasmid. Two plasmid libraries are currently available to the Chodera lab - SGC Oxford and HIP pJP1520. Only SGC Oxford plasmids suitable for E. coli expression are included in this selection procedure.
plasmid_nconflicts Number of conflicts between plasmid and UniProt sequence in the region of the target domain
plasmid_nextraneous_residues Number of plasmid residues outside the target domain region
nPDBs Number of PDB constructs matching the target gene, from any species, and with an E. coli expression system annotation
top_pdb_ID Matching PDB constructs are ranked by auth_score (see below), nextraneous_residues, and nconflicts, and the top-ranked PDB (and chain ID) is selected
top_pdb_expr_tag Type of expression tag detected for top-ranked PDB construct
top_pdb_auth_score Authenticity score assigned to top-ranked PDB construct based on the expression tag detected. Currently this is only used to distinguish between constructs with expression tags (auth_score > 0) and those without (auth_score = 0)
top_pdb_nextraneous_residues Number of PDB construct residues outside the target domain region
family UniProt protein family annotation
top_pdb_taxname Source organism of the top-ranked PDB construct
selected_construct_source Selected constructs will ultimately be full-length SGC Oxford plasmids or PDB constructs (to be subcloned from either SGC Oxford or HIP plasmids).
selected_construct_nextraneous_residues nextraneous_residues for the selected construct

Other notes:

Sort table by clicking on column headers. Shift-click for multicolumn sorting. Drag-click to rearrange columns. Refresh page to reset.
Click on the targetID to see alignments of plasmids and PDB constructs against the target UniProt sequence (kinase catalytic domain highlighted in red).

Table of kinase expression constructs

targetID DB_target_rank plasmid_ID plasmid_source plasmid_nconflicts plasmid_nextraneous_residues nPDBs top_pdb_ID top_pdb_expr_tag top_pdb_auth_score top_pdb_nextraneous_residues family top_pdb_taxname selected_construct_source selected_construct_nextraneous_residues
0 CSK22_HUMAN_D0 154 HsCD00037966 HIP pJP1520 0 65 2 3E3B_X other_extra_seq_Nterm 1 54 -- Human PDB 65
1 MK01_HUMAN_D0 16 HsCD00038083 HIP pJP1520 0 71 61 4FMQ_A TEV_cleaved_Nterm 2 74 CMGC Human PDB 71
2 MK11_HUMAN_D0 159 HsCD00038095 HIP pJP1520 0 80 5 3GP0_A TEV_cleaved_Nterm 2 64 CMGC Human PDB 80
3 MK08_HUMAN_D0 36 HsCD00038084 HIP pJP1520 0 89 32 1UKH_A Histag_Cterm 2 74 CMGC Human PDB 89
4 MK03_HUMAN_D0 52 HsCD00038354 HIP pJP1520 0 90 2 2ZOQ_B other_extra_seq_Nterm 1 94 CMGC Human PDB 90
5 STRAA_HUMAN_D0 402 HsCD00037995 HIP pJP1520 0 92 1 3GNI_B TEV_uncleaved_Nterm 2 79 STE Human PDB 92
6 MAPK2_HUMAN_D0 75 HsCD00037983 HIP pJP1520 0 93 77 2JBO_A TEV_cleaved_Nterm 2 65 CAMK Human PDB 93
7 MKNK2_HUMAN_D0 251 HsCD00037986 HIP pJP1520 3 113 3 2AC5_A TEV_cleaved_Nterm 2 15 CAMK Human PDB 113
8 MP2K4_HUMAN_D0 181 HsCD00038296 HIP pJP1520 0 133 6 3VUT_B Histag_Cterm 2 62 STE Human PDB 133
9 KC1D_HUMAN_D0 93 HsCD00038353 HIP pJP1520 0 140 10 4HNF_B TEV_cleaved_Nterm 2 28 CK1 Human PDB 140
10 MKNK1_HUMAN_D0 214 HsCD00038677 HIP pJP1520 4 140 2 2HW6_B TEV_cleaved_Nterm 2 23 CAMK Human PDB 140
11 KC1G2_HUMAN_D0 238 HsCD00037988 HIP pJP1520 0 145 4 2C47_A TEV_cleaved_Nterm 2 43 CK1 Human PDB 145
12 MST4_HUMAN_D0 308 HsCD00038628 HIP pJP1520 0 165 5 4FZD_B TEV_cleaved_Nterm 2 33 STE Human PDB 165
13 NEK2_HUMAN_D0 89 HsCD00038233 HIP pJP1520 0 181 20 2XKE_A Histag_Cterm 2 16 NEK Human PDB 181
14 VRK3_HUMAN_D0 445 HsCD00037999 HIP pJP1520 0 183 2 2JII_A TEV_uncleaved_Nterm 2 61 CK1 Human PDB 183
15 VRK2_HUMAN_D0 354 HsCD00038025 HIP pJP1520 0 218 2 2V62_B TEV_uncleaved_Nterm 2 55 CK1 Human PDB 218
16 KCC2A_HUMAN_D0 376 HsCD00037978 HIP pJP1520 1 220 3 2VZ6_B TEV_uncleaved_Nterm 2 55 CAMK Human PDB 220
17 PMYT1_HUMAN_D0 304 HsCD00038001 HIP pJP1520 0 248 1 3P1A_A TEV_uncleaved_Nterm 2 62 -- Human PDB 248
18 KCC2G_HUMAN_D0 218 HsCD00038207 HIP pJP1520 1 269 1 2V7O_A TEV_uncleaved_Nterm 2 78 CAMK Human PDB 269
19 E2AK2_HUMAN_D0 135 HsCD00038350 HIP pJP1520 0 279 5 3UIU_A Histag_Cterm 2 35 -- Human PDB 279
20 PAK1_HUMAN_D0 157 HsCD00038597 HIP pJP1520 1 294 17 3Q52_A Histag_Cterm 2 55 STE Human PDB 294
21 DMPK_HUMAN_D0 110 HsCD00038663 HIP pJP1520 2 361 2 2VD5_B TEV_cleaved_Nterm 2 144 AGC Human PDB 361
22 MELK_HUMAN_D0 137 HsCD00038574 HIP pJP1520 0 399 2 4BFM_A Histag_Cterm 2 82 CAMK Mouse PDB 399
23 KS6A3_HUMAN_D0 49 HsCD00038078 HIP pJP1520 0 481 4 4GUE_A TEV_cleaved_Nterm 2 46 AGC Mouse PDB 481
24 HASP_HUMAN_D0 371 HsCD00038762 HIP pJP1520 2 483 7 2VUW_A TEV_cleaved_Nterm 2 22 -- Human PDB 483
25 MARK2_HUMAN_D0 237 HsCD00038251 HIP pJP1520 0 504 20 3IEC_D other_extra_seq_Nterm 1 68 CAMK Human PDB 504
26 BRAF_HUMAN_D0 4 HsCD00038362 HIP pJP1520 0 505 8 4JVG_D TEV_cleaved_Nterm 2 24 TKL Human PDB 505
27 CSKP_HUMAN_D0 111 HsCD00038384 HIP pJP1520 0 633 10 3TAC_A Histag_Nterm 2 97 CAMK Human PDB 633
28 STK10_HUMAN_D0 126 HsCD00038077 HIP pJP1520 0 710 6 4AOT_B TEV_cleaved_Nterm 2 44 STE Human PDB 710
29 EPHB2_HUMAN_D0 91 HsCD00038588 HIP pJP1520 1 723 7 3ZFM_A TEV_cleaved_Nterm 2 35 TK Human PDB 723
30 EPHB3_HUMAN_D0 202 HsCD00038757 HIP pJP1520 0 735 2 3ZFY_B TEV_cleaved_Nterm 2 35 TK Human PDB 735
31 FAK1_HUMAN_D0 32 HsCD00038381 HIP pJP1520 0 747 2 2IJM_B TEV_cleaved_Nterm 2 23 TK Human PDB 747
32 ABL1_HUMAN_D0 12 HsCD00038619 HIP pJP1520 0 879 31 3UE4_A TEV_cleaved_Nterm 2 36 TK Human PDB 879
33 SLK_HUMAN_D0 207 HsCD00038614 HIP pJP1520 1 946 4 2JFL_A TEV_uncleaved_Nterm 2 67 STE Human PDB 946
34 M3K5_HUMAN_D0 151 HsCD00038752 HIP pJP1520 0 1116 4 2CLQ_B TEV_cleaved_Nterm 2 37 STE Human PDB 1116
35 MET_HUMAN_D0 6 HsCD00038375 HIP pJP1520 0 1123 6 4EEV_A Histag_Nterm 2 50 TK Human PDB 1123
36 DAPK1_HUMAN_D0 180 HsCD00038376 HIP pJP1520 1 1168 39 4B4L_A TEV_cleaved_Nterm 2 74 CAMK Human PDB 1168
37 CDK2_HUMAN_D0 26 23777 addgene 0 15 229 4EOO_A TEV_cleaved_Nterm 2 17 CMGC Human PDB 15
38 STK16_HUMAN_D0 302 23565 addgene 1 31 2 2BUJ_B TEV_uncleaved_Nterm 2 44 -- Human PDB 31
39 NEK7_HUMAN_D0 299 23395 addgene 0 37 2 2WQN_A Histag_Cterm 2 45 NEK Human PDB 37
40 CDK6_HUMAN_D0 314 23688 addgene 0 38 2 4EZ5_A Histag_Cterm 2 20 CMGC Human PDB 38
41 CDKL1_HUMAN_D0 361 23389 addgene 23 40 3 4AGU_B TEV_Cterm 2 28 CMGC Human PDB 40
42 PIM1_HUMAN_D0 77 23692 addgene 0 60 91 2O65_A Histag_Cterm 2 41 CAMK Human PDB 60
43 MP2K6_HUMAN_D0 222 23783 addgene 0 72 2 3FME_A TEV_cleaved_Nterm 2 29 STE Human PDB 72
44 MK14_HUMAN_D0 14 23865 addgene 0 75 234 2Y8O_A TEV_cleaved_Nterm 2 78 CMGC Human PDB 75
45 MK13_HUMAN_D0 240 23739 addgene 0 81 4 4EYJ_A Histag_Nterm 2 88 CMGC Human PDB 81
46 AURKB_HUMAN_D0 40 23682 addgene 0 93 1 4AF3_A TEV_cleaved_Nterm 2 42 -- Human PDB 93
47 KAPCA_HUMAN_D0 63 23495 addgene 0 97 162 4IAC_A Histag_Nterm 2 102 AGC Mouse PDB 97
48 MP2K2_HUMAN_D0 88 23555 addgene 0 102 2 1S9I_A Histag_Cterm 2 57 STE Human PDB 102
49 CSK21_HUMAN_D0 62 23678 addgene 0 105 79 3AXW_A other_extra_seq_Nterm 1 55 -- Human PDB 105
50 ST17B_HUMAN_D0 279 23721 addgene 0 111 2 3LM0_A TEV_uncleaved_Nterm 2 67 CAMK Human PDB 111
51 VRK1_HUMAN_D0 384 23496 addgene 0 116 4 3OP5_D TEV_cleaved_Nterm 2 84 CK1 Human PDB 116
52 MAPK3_HUMAN_D0 372 23790 addgene 0 121 4 3FXW_A TEV_uncleaved_Nterm 2 76 CAMK Human PDB 121
53 PHKG2_HUMAN_D0 134 23745 addgene 0 138 4 2Y7J_D TEV_uncleaved_Nterm 2 98 CAMK Human PDB 138
54 KC1E_HUMAN_D0 233 23797 addgene 0 147 14 4HNI_A TEV_cleaved_Nterm 2 28 CK1 Human PDB 147
55 AURKA_HUMAN_D0 43 23532 addgene 0 153 87 2NP8_A TEV_cleaved_Nterm 2 22 -- Human PDB 153
56 KC1G3_HUMAN_D0 294 23400 addgene 0 153 9 2CHL_A TEV_uncleaved_Nterm 2 81 CK1 Human PDB 153
57 CLK1_HUMAN_D0 171 23817 addgene 0 167 2 2VAG_A TEV_cleaved_Nterm 2 23 CMGC Human PDB 167
58 CLK3_HUMAN_D0 223 23753 addgene 0 173 6 2WU7_A TEV_uncleaved_Nterm 2 65 CMGC Human PDB 173
59 STK24_HUMAN_D0 274 23595 addgene 0 180 11 3ZHP_C TEV_uncleaved_Nterm 2 44 STE Human PDB 180
60 DAPK3_HUMAN_D0 198 23436 addgene 0 192 6 3BHY_A TEV_cleaved_Nterm 2 21 CAMK Human PDB 192
61 CSK_HUMAN_D0 148 23941 addgene 0 195 4 3D7T_A other_extra_seq_Nterm 1 15 TK Human PDB 195
62 CDK16_HUMAN_D0 257 23754 addgene 0 214 1 3MTL_A Histag_Cterm 2 43 CMGC Human PDB 214
63 KCC4_HUMAN_D0 224 23812 addgene 0 218 1 2W4O_A TEV_uncleaved_Nterm 2 95 CAMK Human PDB 218
64 KCC2D_HUMAN_D0 172 23814 addgene 0 219 3 2VN9_A TEV_cleaved_Nterm 2 43 CAMK Human PDB 219
65 KCC1G_HUMAN_D0 305 23813 addgene 0 221 2 2JAM_A TEV_cleaved_Nterm 2 50 CAMK Human PDB 221
66 STK3_HUMAN_D0 219 23818 addgene 0 239 10 4LG4_B TEV_cleaved_Nterm 2 48 STE Human PDB 239
67 KCC2B_HUMAN_D0 249 23820 addgene 0 244 4 3BHH_D TEV_cleaved_Nterm 2 37 CAMK Human PDB 244
68 CHK2_HUMAN_D0 24 23843 addgene 0 276 44 2CN5_A other_extra_seq_Nterm 1 63 CAMK Human PDB 276
69 SRC_HUMAN_D0 10 23934 addgene 0 282 97 4MXO_A TEV_cleaved_Nterm 2 33 TK Human PDB 282
70 DYRK2_HUMAN_D0 250 23690 addgene 0 287 3 4AZF_A TEV_uncleaved_Nterm 2 104 CMGC Human PDB 287
71 AAPK1_HUMAN_D0 183 23871 addgene 0 297 1 4CFH_A TEV_uncleaved_Nterm 2 241 CAMK Rat PDB 297
72 AAPK2_HUMAN_D0 194 23671 addgene 0 299 5 2H6D_A TEV_cleaved_Nterm 2 24 CAMK Human PDB 299
73 PAK4_HUMAN_D0 162 23713 addgene 0 339 24 2J0I_A TEV_cleaved_Nterm 2 52 STE Human PDB 339
74 PAK6_HUMAN_D0 282 23833 addgene 0 429 3 2C30_A TEV_uncleaved_Nterm 2 70 STE Human PDB 429
75 PLK2_HUMAN_D0 190 23691 addgene 0 432 5 4I5P_A Histag_Nterm 2 56 -- Human PDB 432
76 PAK7_HUMAN_D0 236 23850 addgene 0 467 2 2F57_B TEV_uncleaved_Nterm 2 66 STE Human PDB 467
77 MARK3_HUMAN_D0 366 23716 addgene 0 477 4 2QNJ_A other_extra_seq_Nterm 1 77 CAMK Human PDB 477
78 FGFR3_HUMAN_D0 13 23933 addgene 0 516 1 4K33_A Histag_Nterm 2 38 TK Human PDB 516
79 FGFR1_HUMAN_D0 11 23922 addgene 0 530 28 3KY2_A Histag_Nterm 2 30 TK Human PDB 530
80 FGFR2_HUMAN_D0 17 23904 addgene 0 550 40 3RI1_B TEV_cleaved_Nterm 2 26 TK Human PDB 550
81 FES_HUMAN_D0 119 23876 addgene 0 560 4 3CBL_A TEV_cleaved_Nterm 2 116 TK Human PDB 560
82 TTK_HUMAN_D0 158 23857 addgene 0 590 20 3H9F_A TEV_uncleaved_Nterm 2 47 -- Human PDB 590
83 EPHB4_HUMAN_D0 96 23896 addgene 0 702 2 3ZEW_A TEV_cleaved_Nterm 2 21 TK Human PDB 702
84 EPHB1_HUMAN_D0 182 23930 addgene 0 720 9 3ZFX_F TEV_cleaved_Nterm 2 35 TK Human PDB 720
85 EPHA3_HUMAN_D0 95 23911 addgene 0 721 21 4GK2_A Histag_Nterm 2 100 TK Human PDB 721
86 MERTK_HUMAN_D0 98 23900 addgene 0 727 12 3BPR_B Histag_Nterm 2 42 TK Human PDB 727
87 BMPR2_HUMAN_D0 78 23669 addgene 0 736 2 3G2F_A Histag_Cterm 2 35 TKL Human PDB 736
88 FAK2_HUMAN_D0 76 23898 addgene 0 750 2 3CC6_A TEV_cleaved_Nterm 2 23 TK Human PDB 750
89 VGFR1_HUMAN_D0 19 23912 addgene 0 1006 1 3HNG_A TEV_cleaved_Nterm 2 29 TK Human PDB 1006