4QTE - JenaLib

Title :   STRUCTURE OF ERK2 IN COMPLEX WITH VTX-11E, 4-{2-[(2-CHLORO-4-FLUOROPHENYL)AMINO]-5-METHYLPYRIMIDIN-4-YL}-N-[(1S)-1-(3-CHLOROPHENYL)-2-HYDROXYETHYL]-1H-PYRROLE-2-CARBOXAMIDE

Authors :   A. Chaikuad, P. Savitsky, F. Von Delft, C. H. Arrowsmith, A. M. Edwards C. Bountra, S. Knapp, Structural Genomics Consortium (Sgc)

Date :   07 Jul 14 (Deposition) - 23 Jul 14 (Release) - 24 Sep 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (2x)

Keywords :   Structural Genomics, Structural Genomics Consortium, Sgc, Transferase, Kinase, Mapk, Signalling, Inhibitor, Allosteric, Structural Genomics Consortium (Sgc), Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Chaikuad, E. M C Tacconi, J. Zimmer, Y. Liang, N. S. Gray, M. Tarsounas, S. Knapp
A Unique Inhibitor Binding Site In Erk1/2 Is Associated Wit Slow Binding Kinetics.
Nat. Chem. Biol. V. 10 853 2014
PubMed-ID: 25195011 | Reference-DOI: 10.1038/NCHEMBIO.1629

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 30)

Asymmetric Unit (4, 30)

No.	Name	Count	Type	Full Name
1	390	1	Ligand/Ion	4-{2-[(2-CHLORO-4-FLUOROPHENYL)AMINO]-5-METHYLPYRIMIDIN-4-YL}-N-[(1S)-1-(3-CHLOROPHENYL)-2-HYDROXYETHYL]-1H-PYRROLE-2-CARBOXAMIDE
2	CL	2	Ligand/Ion	CHLORIDE ION
3	EDO	22	Ligand/Ion	1,2-ETHANEDIOL
4	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 28)

No.	Name	Count	Type	Full Name
1	390	1	Ligand/Ion	4-{2-[(2-CHLORO-4-FLUOROPHENYL)AMINO]-5-METHYLPYRIMIDIN-4-YL}-N-[(1S)-1-(3-CHLOROPHENYL)-2-HYDROXYETHYL]-1H-PYRROLE-2-CARBOXAMIDE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EDO	22	Ligand/Ion	1,2-ETHANEDIOL
4	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 56)

No.	Name	Count	Type	Full Name
1	390	2	Ligand/Ion	4-{2-[(2-CHLORO-4-FLUOROPHENYL)AMINO]-5-METHYLPYRIMIDIN-4-YL}-N-[(1S)-1-(3-CHLOROPHENYL)-2-HYDROXYETHYL]-1H-PYRROLE-2-CARBOXAMIDE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EDO	44	Ligand/Ion	1,2-ETHANEDIOL
4	SO4	10	Ligand/Ion	SULFATE ION

Sites (30, 30)

Asymmetric Unit (30, 30)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:82 , TYR A:128 , GLN A:132 , ARG A:135 , LYS A:259 , HOH A:553 , HOH A:795	BINDING SITE FOR RESIDUE EDO A 401
02	AC2	SOFTWARE	ARG A:301 , GLU A:303 , GLN A:306 , HOH A:799 , HOH A:800 , HOH A:924	BINDING SITE FOR RESIDUE EDO A 402
03	AC3	SOFTWARE	GLY A:182 , TYR A:316 , HOH A:544 , HOH A:882	BINDING SITE FOR RESIDUE EDO A 403
04	AC4	SOFTWARE	ASN A:123 , ASN A:281 , ASP A:283 , HOH A:949	BINDING SITE FOR RESIDUE EDO A 404
05	AC5	SOFTWARE	HIS A:299 , HOH A:852	BINDING SITE FOR RESIDUE EDO A 405
06	AC6	SOFTWARE	LEU A:116 , GLU A:220 , ASN A:224 , ARG A:225 , PRO A:226 , HOH A:588 , HOH A:655 , HOH A:833	BINDING SITE FOR RESIDUE EDO A 406
07	AC7	SOFTWARE	ASN A:158 , THR A:159 , HOH A:666 , HOH A:839 , HOH A:930	BINDING SITE FOR RESIDUE EDO A 407
08	AC8	SOFTWARE	TYR A:113 , LYS A:151 , SER A:153 , THR A:190 , EDO A:415 , HOH A:526 , HOH A:826	BINDING SITE FOR RESIDUE EDO A 408
09	AC9	SOFTWARE	GLN A:62 , THR A:63 , HOH A:703	BINDING SITE FOR RESIDUE EDO A 409
10	BC1	SOFTWARE	LYS A:330 , PHE A:331 , HOH A:745 , HOH A:872	BINDING SITE FOR RESIDUE EDO A 410
11	BC2	SOFTWARE	HIS A:120 , LEU A:121 , MET A:221 , LEU A:222 , ASN A:224 , HOH A:884	BINDING SITE FOR RESIDUE EDO A 411
12	BC3	SOFTWARE	TYR A:316	BINDING SITE FOR RESIDUE EDO A 412
13	BC4	SOFTWARE	LYS A:272 , GLU A:326 , HOH A:578	BINDING SITE FOR RESIDUE EDO A 413
14	BC5	SOFTWARE	ARG A:277 , GLU A:305 , HOH A:567 , HOH A:581 , HOH A:787 , HOH A:893	BINDING SITE FOR RESIDUE EDO A 414
15	BC6	SOFTWARE	LYS A:151 , THR A:190 , EDO A:408 , HOH A:564	BINDING SITE FOR RESIDUE EDO A 415
16	BC7	SOFTWARE	LYS A:207 , HOH A:659 , HOH A:776 , HOH A:786 , HOH A:893	BINDING SITE FOR RESIDUE EDO A 416
17	BC8	SOFTWARE	LEU A:264 , LEU A:265 , LEU A:267 , HIS A:269 , HOH A:652	BINDING SITE FOR RESIDUE EDO A 417
18	BC9	SOFTWARE	PRO A:268 , HIS A:269 , LYS A:270 , HOH A:805 , HOH A:806 , HOH A:956	BINDING SITE FOR RESIDUE EDO A 418
19	CC1	SOFTWARE	SER A:266 , HOH A:901 , HOH A:919	BINDING SITE FOR RESIDUE EDO A 419
20	CC2	SOFTWARE	EDO A:421 , HOH A:641 , HOH A:898	BINDING SITE FOR RESIDUE EDO A 420
21	CC3	SOFTWARE	GLU A:314 , GLN A:315 , EDO A:420 , HOH A:620 , HOH A:664	BINDING SITE FOR RESIDUE EDO A 421
22	CC4	SOFTWARE	LEU A:116 , ASN A:224 , HOH A:655 , HOH A:702	BINDING SITE FOR RESIDUE EDO A 422
23	CC5	SOFTWARE	ARG A:191 , ARG A:194 , TYR A:233 , HOH A:656 , HOH A:668 , HOH A:698 , HOH A:775 , HOH A:796 , HOH A:856	BINDING SITE FOR RESIDUE SO4 A 423
24	CC6	SOFTWARE	ASP A:283 , LYS A:285 , PRO A:311 , TYR A:312 , GLN A:315 , HOH A:647 , HOH A:733 , HOH A:947	BINDING SITE FOR RESIDUE SO4 A 424
25	CC7	SOFTWARE	ARG A:77 , TYR A:139 , ASN A:271 , ALA A:325 , GLU A:326 , HOH A:629 , HOH A:763 , HOH A:905	BINDING SITE FOR RESIDUE SO4 A 425
26	CC8	SOFTWARE	VAL A:14 , ARG A:15 , SER A:29 , TYR A:30 , HOH A:932	BINDING SITE FOR RESIDUE SO4 A 426
27	CC9	SOFTWARE	HIS A:232 , LEU A:234	BINDING SITE FOR RESIDUE CL A 427
28	DC1	SOFTWARE	HIS A:180 , ASN A:201 , ILE A:256 , ASN A:257	BINDING SITE FOR RESIDUE CL A 428
29	DC2	SOFTWARE	ARG A:148 , ARG A:172 , HOH A:704 , HOH A:952 , HOH A:953	BINDING SITE FOR RESIDUE SO4 A 429
30	DC3	SOFTWARE	ILE A:31 , GLY A:34 , TYR A:36 , GLY A:37 , MET A:38 , VAL A:39 , ALA A:52 , LYS A:54 , GLN A:105 , ASP A:106 , MET A:108 , GLU A:109 , ASP A:111 , LYS A:114 , ASN A:154 , LEU A:156 , ASP A:167 , HOH A:523 , HOH A:600 , HOH A:628 , HOH A:823	BINDING SITE FOR RESIDUE 390 A 430

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:348
                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee..eee.....eeeeeeeeee..eeeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhhh.........eee..........eeeeee...eehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.hhhhh..........hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhhh..hhhhhhhhhhh......hhhhhh...hhhhhhhhhhhh........hhhhhhhhhhhh...hhhhh................hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4qte A  11 PEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGY 358
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (107, 107)

Visualization

Interactive Views

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		390	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]
		BC9	[ RasMol ]	+environment [ RasMol ]
		CC1	[ RasMol ]	+environment [ RasMol ]
		CC2	[ RasMol ]	+environment [ RasMol ]
		CC3	[ RasMol ]	+environment [ RasMol ]
		CC4	[ RasMol ]	+environment [ RasMol ]
		CC5	[ RasMol ]	+environment [ RasMol ]
		CC6	[ RasMol ]	+environment [ RasMol ]
		CC7	[ RasMol ]	+environment [ RasMol ]
		CC8	[ RasMol ]	+environment [ RasMol ]
		CC9	[ RasMol ]	+environment [ RasMol ]
		DC1	[ RasMol ]	+environment [ RasMol ]
		DC2	[ RasMol ]	+environment [ RasMol ]
		DC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:22 - Pro A:23	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	4qte
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	MK01_HUMAN \| P28482
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.7.11.24
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description