Predikin Prediction Server

Monday, 23 November 2009

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Protein kinases in the PDB

For this project, we wanted to identify all of the protein kinase structures in the PDB and create a summary table with links to sequence and structure. An outline of the procedure:

Download file of all PDB chain sequences in fasta format from NCBI
Use HMMER program hmmsearch to search the sequences for the protein kinase catalytic domain
Extract kinase sequences and cluster using CD-HIT with 90% redundancy
Write a parser to combine all the output and generate a summary table

The original data are here and you can also read a more detailed account of the bioinformatics.

Here's the summary table:

Cluster	Type	KSD Name	PANTHER NAME	GI	PDB
000	Ser/Thr	GRK-I	BETA-ADRENERGIC RECEPTOR KINASE	31615810	1OMW
001	Ser/Thr	GRK-II	G PROTEIN-COUPLED RECEPTOR KINASE 1,2,4,5,6	99031797	2ACX
				109157762	2G2F
				126030685	2HYY
				88192844	2F4J
				114794378	2HIW
				126030689	2HZ0
				30749934	1OPK
				119389607	2GQG
002	Tyr	Abl	PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL1	30749935	1OPL
				93279684	2FO0
				10835731	1FPU
				126030694	2HZI
				109157754	2G1T
				99031637	1YI6
				71041981	1Y57
				118137342	2BDF
				134104465	2HWO
				20151029	1KSW
003	Tyr	Src	PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC	119389672	2H8H
				2392337	1FMK
				88191855	1YOL
				2780916	2PTK
				88191853	1YOJ
004	Ser/Thr	MLCK/Twitchin	MYOSIN LIGHT CHAIN KINASE-RELATED	1942207	1KOA
005	Tyr	Src	TYROSINE-PROTEIN KINASE HCK	5542349	1QCF
				2194103	1AD5
				114794401	2HK5
006	Tyr	Csk	TYROSINE PROTEIN KINASE CSK (PTK GROUP III)	20150729	1K9A
				6435671	1BYG
				42543881	1UV5
				34810589	1O9U
				52695345	1Q5K
				24987247	1GNG
				56553624	1R0E
				18158777	1I09
				38492874	1PYX
				18655515	1H8F
007	CMGC	GSK3-II	GLYCOGEN SYNTHASE KINASE 3-RELATED (GSK3) (CMGC GROUP III)	38492892	1Q3D
				126031626	2OK1
				116666756	2B1P
				34809763	1PMN
				99032346	2G01
008	CMGC	ERK-II	JNK	5542282	1JNK
				134105020	2O0U
				66361773	1UKH
				119389382	2EXC
009	Ser/Thr	MDK	RHO-ASSOCIATED, COILED-COIL CONTAINING PROTEIN KINASE	83754946	2ESM
				38492554	1NXK
				24158794	1KWP
010	Ser/Thr	MAPKAP	MAP KINASE-ACTIVATED PROTEIN KINASE (MAPKAPK)	126031692	2ONL
011	Ser/Thr	MDK	RHO-ASSOCIATED, COILED-COIL CONTAINING PROTEIN KINASE	99032135	2F2U
012	CMGC	SRPK1	SRPK	82407376	1WBP
013	Ser/Thr	MLCK/Twitchin	MYOSIN LIGHT CHAIN KINASE-RELATED	1942208	1KOB
				110590383	2GPH
				78100780	1TVO
014	CMGC	ERK/MAPK	MITOGEN-ACTIVATED PROTEIN KINASE 1,3 (ERK1,2)	5542329	1PME
				1942172	1GOL
				3318705	2ERK
				126031620	2OJG
				2194078	1ERK
				85543925	1WZY
				83754340	2BAJ
				37927357	1OZ1
				119389523	2FST
				4929863	1A9U
015	CMGC	ERK-II	P38 MAPK	2914479	1P38
				119389520	2FSL
				11513304	1DI9
				109158061	2GTM
				83754342	2BAL
				34810067	1OVE
				2554639	1WFC
				67464491	1YWR
				83754345	2BAQ
				99032559	2GHL
				99032503	2GFS
				67464490	1YW2
				3212538	1IAN
				119389522	2FSO
				78101173	1ZZL
				22219219	1LEW
				37928043	1Q8Y
016	CMGC	SRPK1	SRPK	13399615	1HOW
017	Tyr	Eph/Elk/Eck	EPHRIN TYPE-A RECEPTOR	110590407	2GSF
018	CMGC	ERK-II	P38 MAPK	8569500	1CM8
019	Tyr	PDGFR	VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2	71041982	1Y6A
020	Ser/Thr	PKC/PKA	PROTEIN KINASE C (PKC)	78101111	1ZRZ
021	Ser/Thr	CaMK-III	CALCIUM/CALMODULIN DEPENDENT PROTEIN KINASE II	85544276	2BDW
				83754974	2EU9
022	CMGC	LAMMER	CLK3	83755011	2EXE
023	Ser/Thr	PKC/PKA	RIBOSOMAL PROTEIN S6 KINASE ALPHA 4,5	50514024	1VZO
024	Ser/Thr	MEK/Ste7	MITOGEN ACTIVATED PROTEIN KINASE KINASE 2, MAPKK2, MEK2	56966000	1S9I
				85544239	2B9H
025	CMGC	ERK-I	MITOGEN-ACTIVATED PROTEIN KINASE 1,3 (ERK1,2)	85544238	2B9F
				119389443	2F9G
026	Ser/Thr	PKC/PKA	PROTEIN KINASE C (PKC)	119390008	2I0E
				134104655	2J5F
027	Tyr	EGFR-II	EPIDERMAL GROWTH FACTOR RECEPTOR	58177366	1XKK
				110590401	2GS2
				23200417	1M14
				110590405	2GS7
				134104654	2J5E
				20151205	1L3R
				78100920	1XH9
				2098410	1YDT
				109157919	2GNJ
				50513587	1SMH
				576052	1CMK
				78100916	1XH7
				2982123	1STC
				61680034	1U7E
				28948416	1J3H
				83754461	2C1A
				49259182	1SZM
				37927861	1Q61
				134104896	2JDT
				109157911	2GNF
				109157913	2GNG
				493956	1CTP
				134104894	2JDS
				14719578	1JBP
				349816	1APM
				34810567	1Q24
				67464135	1SYK
				40889426	1Q8W
				48425310	1RDQ
				2981777	1BKX
				230462	2CPK
				83754941	2ERZ
				62737996	1SVH
				2914581	1FMO
028	Ser/Thr	cAMP-II	CAMP-DEPENDENT PROTEIN KINASE, CATALYTIC SUBUNIT (PKA C)	110591345	2F7E
				114794862	2IZR
029	Ser/Thr	CK1-I	CASEIN KINASE	93279163	2CHL
				114794045	2GCD
030	Ser/Thr	KFC	STE20-LIKE KINASE	56554138	1U5Q
031	CMGC	CDK5	CAK1	58176911	1UA2
032	Ser/Thr	PKC/PKA	PROTEIN KINASE C (PKC)	56554577	1XJD
033	Tyr	PDGFR	FL CYTOKINE RECEPTOR (TYROSINE-PROTEIN KINASE RECEPTOR FLT3)	42543565	1RJB
034	Tyr	Trk/ROR	MUSCLE, SKELETAL RECEPTOR TYROSINE PROTEIN KINASE	24158900	1LUF
				51247205	1PY5
				60593446	1RW8
035	Ser/Thr	Alk/Daf1	TRANSFORMING GROWTH FACTOR-BETA RECEPTOR TYPE I AND II	5542075	1B6C
				52696121	1VJY
				37926827	1MRV
				27066378	1O6K
				31615318	1GZN
				27066381	1O6L
				31615317	1GZK
036	Ser/Thr	Akt/Rac	RAC SERINE/THREONINE KINASE	134104886	2JDO
037	Ser/Thr	MEK/Ste7	MITOGEN ACTIVATED PROTEIN KINASE KINASE 1, MAPKK1, MEK1	56966002	1S9J
038	CMGC	LAMMER	CLK4	66361317	1Z57
				33358120	1PJK
				61680730	1YMI
039	CMGC	CK2	CASEIN KINASE II, ALPHA CHAIN (CMGC GROUP IV)	20150571	1JWH
				34810211	1NA7
040	Tyr	PDGFR	MACROPHAGE COLONY-STIMULATING FACTOR RECEPTOR	119390010	2I0V
				119390020	2I1M
				126031591	2OGV
041	Ser/Thr	No ann.	CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE 1 (CAMKI)	134104767	2JC6
042	Tyr	Eph/Elk/Eck	EPHRIN TYPE-A RECEPTOR 1,2	37926807	1MQB
				66361219	1YWV
				61680889	2BIK
043	Ser/Thr	PIM	SERINE/THREONINE PROTEIN KINASE	126031488	2OBJ
				60594373	1YHS
				134104604	2J2I
				56967222	1XQZ
				61680891	2BIL
				56967283	1XWS
				66361235	1YXS
044	CMGC	CK2	CASEIN KINASE II, ALPHA CHAIN (CMGC GROUP IV)	13096757	1DS5
				7766821	1DAW
				33357307	1M2P
045	Ser/Thr	No ann.	CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE 1 (CAMKI)	3114436	1A06
046	Tyr	PDGFR	MAST/STEM CELL GROWTH FACTOR RECEPTOR (PROTO-ONCOGENE TYROSINE-PROTEIN KINASE KIT) (C-KIT)	50513700	1T45
				34810084	1PKG
				50513701	1T46
047	Ser/Thr	CaMK-II	SERINE/THREONINE-PROTEIN KINASE CHK2 (CDS1)	110591043	2CN5
048	Ser/Thr	Kin2	MAP/MICROTUBULE AFFINITY-REGULATING KINASE 2,4	112491250	2HAK
049	Tyr	Tie/Tck	ANGIOPOIETIN 1 RECEPTOR (TYROSINE-PROTEIN KINASE RECEPTOR TIE-2)	15988250	1FVR
				90108642	1ZMV
				90108644	1ZMW
050	Ser/Thr	Kin2	MAP/MICROTUBULE AFFINITY-REGULATING KINASE 2,4	90108640	1ZMU
				90108519	1Y8G
				20150484	1JOW
051	CMGC	CDK4/CDK6	CDK4/6	4389286	1BI8
				126031065	2JA0
				134104916	2JFM
052	Ser/Thr	GC Kinase	SLK PROTEIN	118138635	2J51
				134104915	2JFL
053	Tyr	IRK	INSULIN-LIKE GROWTH FACTOR-1 RECEPTOR	28373614	1M7N
				30750130	1P4O
				20663951	1JQH
				17943043	1K3A
054	Tyr	MLCK/Twitchin	MYOSIN LIGHT CHAIN KINASE	5542491	1TKI
				118137254	1ZWS
				118137263	2A27
				118137271	2A2A
055	Ser/Thr	TRAD	DEATH- ASSOCIATED PROTEIN KINASE	88191740	1WMK
				118137243	1Z9X
056	Ser/Thr	KFC	P21-ACTIVATED KINASE, PAK	90108952	2C30
057	CMGC	ERK/MAPK	MITOGEN-ACTIVATED PROTEIN KINASE 6 (ERK3)	116668022	2I6L
058	Ser/Thr	cAMP-II	CAMP-DEPENDENT PROTEIN KINASE, CATALYTIC SUBUNIT (PKA C)	14719777	1FOT
059	Tyr	Axl	MET PROTO-ONCOGENE HEPATOCYTE GROWTH FACTOR RECEPTOR-RELATED	93279833	2G15
				37928127	1R0P
060	Ser/Thr	CK1-I	CASEIN KINASE	1311054	1CKJ
061	CMGC	PKL12	SERINE/THREONINE KINASE 16 (STK16 )	73536291	2BUJ
062	Ser/Thr	PAK/STE20	P21-ACTIVATED KINASE, PAK	85544594	2F57
				75765648	1YWN
063	Tyr	PDGFR	VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2	7546569	1VR2
064	Tyr	FGFR-I	FIBROBLAST GROWTH FACTOR RECEPTOR	22218646	1GJO
				78101293	2AC3
065	Ser/Thr	MAPK/GRK7	MAP KINASE-INTERACTING SERINE/THREONINE KINASE	78101295	2AC5
				114794791	2IVT
066	Tyr	FGFR-II	PROTO-ONCOGENE RECEPTOR TYROSINE PROTEIN KINASE RET	114794793	2IVV
				114794789	2IVS
067	Ser/Thr	CK1-I	CASEIN KINASE	83754634	2C47
				134104447	2HEN
068	Tyr	Eph/Elk/Eck	EPHRIN TYPE-B RECEPTOR	15988071	1JPA
069	Ser/Thr	PIM	SERINE/THREONINE PROTEIN KINASE	114794810	2IWI
				28374107	1O6Y
070	Ser/Thr	PKN1	MAPKK-RELATED SERINE/THREONINE PROTEIN KINASES	28948659	1MRU
071	Tyr	FGFR-I	FIBROBLAST GROWTH FACTOR RECEPTOR	2392334	1FGK
				66361318	1Z5M
				47169288	1UU9
				61680895	2BIY
				34811348	1H1W
072	Ser/Thr	PKB	3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1	47169285	1UU3
073	Ser/Thr	CK1-I	CASEIN KINASE	110591041	2CMW
				34809870	1OIT
				33356961	1GZ8
				6730495	1QMZ
				1942427	1FIN
				24158643	1H1P
				116668171	2IW8
074	CMGC	CDK	CELL DIVISION CONTROL PROTEIN 2 (P34 PROTEIN KINASE) (CYCLIN-DEPENDENT KINASE 1) (CDK1)	50514017	1VYW
				4139569	1B38
				1942625	1JST
				34810054	1OGU
				40889309	1PF8
				61680193	1W98
				116668167	2IW6
				34809859	1H01
				16975317	1E9H
				34809869	1OIR
				18655411	1GII
075	Ser/Thr	No ann.	MAPKK-RELATED SERINE/THREONINE PROTEIN KINASES	112491038	2H34
076	Ser/Thr	Ctr1/DPYK1	TAK1	99032119	2EVA
077	Ser/Thr	MAPK/GRK7	MAP KINASE-INTERACTING SERINE/THREONINE KINASE	114794592	2HW6
				122920981	2NRU
078	Ser/Thr	No ann.	INTERLEUKIN-1 RECEPTOR-ASSOCIATED KINASE-4	122920986	2NRY
				40889699	1RQQ
				999510	1IRK
				34811267	1P14
079	Tyr	IRK	INSULIN RECEPTOR	2780855	1IR3
				13399500	1I44
				88192581	2C6E
				38492660	1OL6
				119390407	2J50
				38492658	1OL5
				119390405	2J4Z
				37926805	1MQ4
080	Ser/Thr	Aurora	AURORA KINASE-RELATED	62739016	2BMC
				30749504	1MUO
				88192580	2C6D
081	Tyr	Eph/Elk/Eck	EPHRIN TYPE-A RECEPTOR	134104446	2HEL
082	Ser/Thr	MLCK/Twitchin	DEATH- ASSOCIATED PROTEIN KINASE	119390449	2J90
				110590709	1YRP
				71042556	1ZY4
083	Ser/Thr	No ann.	INTERFERON-INDUCED, DOUBLE-STRANDED RNA-ACTIVATED PROTEIN KINASE (P1/EIF-2A PROTEIN KINASE)	71042560	1ZYC
				71042541	1ZXE
084	Ser/Thr	PAK/STE20	P21-ACTIVATED KINASE, PAK	90109122	2CDZ
				73536296	2BVA
085	Ser/Thr	GC Kinase	POLO-LIKE KINASE KINASE 1	119390433	2J7T
				1421245	2CSN
086	Ser/Thr	CK1-I	CASEIN KINASE	1127277	1CSN
087	Ser/Thr	PhB	PHOSPHORYLASE KINASE, GAMMA 2	1827741	1PHK
				4389105	2PHK
				6730463	1QL6
				67463908	1YHV
088	Ser/Thr	PAK/STE20	P21-ACTIVATED KINASE, PAK	9256908	1F3M
				116666738	2AYP
089	Ser/Thr	Chk1	CHECKPOINT KINASE 1	67464423	2BR1
				110590725	1ZLT
				14278486	1IA8
				110590744	1ZYS
				122920166	2FGA
090	Ser/Thr	MEKK/STE11	MITOGEN ACTIVATED PROTEIN KINASE KINASE KINASE 5, MAPKKK5, MEKK5	109157363	2CLQ
091	Ser/Thr	TRAD	DEATH- ASSOCIATED PROTEIN KINASE	20150170	1IG1
				99031616	1WVW
				20150446	1JKK
				55669538	1P4F
092	Tyr	JAK/TYK2	TYROSINE-PROTEIN KINASE JAK2	88192291	2B7A
				56966251	1UNG
093	CMGC	CDK	CDK5	23200128	1H4L
				52695995	1U46
094	Tyr	Ack	ACK FAMILY (CDC42-ASSOCIATED TYROSINE PROTEIN KINASE) (PTK GROUP XIII)	52696004	1U54
095	Tyr	SYK/ZAP70	TYROSINE-PROTEIN KINASE SYK (SPLEEN TYROSINE KINASE)	56554454	1XBA
096	Ser/Thr	WNK	SERINE/THREONINE-PROTEIN KINASE WNK 1,3,4	51247551	1T4H
097	Tyr	JAK/TYK2	TYROSINE-PROTEIN KINASE JAK3	67463918	1YVJ
098	Ser/Thr	Wee1	WEE1 PROTEIN KINASE-RELATED	71041942	1X8B
				42543186	1OB3
099	CMGC	CDK	CDK5	48425852	1V0O
				47169418	1V0B
100	Tyr	SYK/ZAP70	TYROSINE-PROTEIN KINASE ZAP-70	52696010	1U59
				73536251	2BFY
101	Ser/Thr	Aurora	AURORA KINASE-RELATED	73536247	2BFX
102	Ser/Thr	PKR	EUKARYOTIC TRANSLATION INITIATION FACTOR 2-ALPHA KINASE (EIF2-ALPHA KINASE)-RELATED	78101184	2A19
103	Tyr	Src	PROTO-ONCOGENE TYROSINE-PROTEIN KINASE FYN	110591271	2DQ7
				118137641	2ETM
104	Tyr	SYK/ZAP70	FOCAL ADHESION KINASE	37926803	1MP8
				47169342	1UWJ
				47169340	1UWH
105	Ser/Thr	Raf	B-RAF	122920151	2FB8
				134105145	2OF2
				134105147	2OFU
				8569365	1QPE
				134105148	2OFV
106	Tyr	Src	PROTO-ONCOGENE TYROSINE-PROTEIN KINASE LCK	8569441	1QPD
				2781151	3LCK
				134105153	2OG8
107	Ser/Thr	NimA-I	NIMA-RELATED PROTEIN KINASE, NEK	122920883	2JAV
108	Ser/Thr	cAMP-III	5-AMP-ACTIVATED PROTEIN KINASE (AMPK) (SNF1-RELATED)	110590560	2H6D
109	Ser/Thr	KIN1/SNF1/Nim1	5-AMP-ACTIVATED PROTEIN KINASE (AMPK) (SNF1-RELATED)	93279511	2FH9
110	Tyr	Tec/Atk	TYROSINE-PROTEIN KINASE ITK/TSK	51247402	1SM2
111	Tyr	Tec/Atk	TYROSINE-PROTEIN KINASE BTK	21730412	1K2P
112	Ser/Thr	KIN1/SNF1/Nim1	5-AMP-ACTIVATED PROTEIN KINASE (AMPK) (SNF1-RELATED)	85544717	2EUE
				85544716	2EUE

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