4LV6 - JenaLib

Title :   CRYSTAL STRUCTURE OF SMALL MOLECULE DISULFIDE 4 COVALENTLY BOUND TO K-RAS G12C

Authors :   J. M. Ostrem, U. Peters, M. L. Sos, J. A. Wells, K. M. Shokat

Date :   26 Jul 13 (Deposition) - 27 Nov 13 (Release) - 18 Dec 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: B  (1x)

Keywords :   Gtpase, Gdp Bound, Small Molecule Inhibitor, Covalent Binder, Signaling Protein-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. M. Ostrem, U. Peters, M. L. Sos, J. A. Wells, K. M. Shokat
K-Ras(G12C) Inhibitors Allosterically Control Gtp Affinity And Effector Interactions.
Nature V. 503 548 2013
PubMed-ID: 24256730 | Reference-DOI: 10.1038/NATURE12796

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	20H	2	Ligand/Ion	1-[(2,4-DICHLOROPHENOXY)ACETYL]-N-(2-SULFANYLETHYL)PIPERIDINE-4-CARBOXAMIDE
2	CA	4	Ligand/Ion	CALCIUM ION
3	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	20H	2	Ligand/Ion	1-[(2,4-DICHLOROPHENOXY)ACETYL]-N-(2-SULFANYLETHYL)PIPERIDINE-4-CARBOXAMIDE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	20H	1	Ligand/Ion	1-[(2,4-DICHLOROPHENOXY)ACETYL]-N-(2-SULFANYLETHYL)PIPERIDINE-4-CARBOXAMIDE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	20H	1	Ligand/Ion	1-[(2,4-DICHLOROPHENOXY)ACETYL]-N-(2-SULFANYLETHYL)PIPERIDINE-4-CARBOXAMIDE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:17 , GDP A:204 , HOH A:301 , HOH A:302 , HOH A:303 , HOH A:306	BINDING SITE FOR RESIDUE CA A 201
2	AC2	SOFTWARE	GLU A:63 , GLY A:138 , HOH A:309 , HOH A:320 , HOH A:325 , HOH A:340	BINDING SITE FOR RESIDUE CA A 202
3	AC3	SOFTWARE	VAL A:9 , GLY A:10 , CYS A:12 , ALA A:59 , GLY A:60 , GLN A:61 , ARG A:68 , MET A:72 , TYR A:96 , ILE A:100 , HOH A:310 , HOH A:316 , HOH A:425	BINDING SITE FOR RESIDUE 20H A 203
4	AC4	SOFTWARE	GLY A:13 , VAL A:14 , GLY A:15 , LYS A:16 , SER A:17 , ALA A:18 , PHE A:28 , VAL A:29 , ASP A:30 , ARG A:73 , ASN A:116 , LYS A:117 , ASP A:119 , LEU A:120 , SER A:145 , ALA A:146 , LYS A:147 , CA A:201 , HOH A:301 , HOH A:302 , HOH A:343 , HOH A:347 , HOH A:397	BINDING SITE FOR RESIDUE GDP A 204
5	AC5	SOFTWARE	SER B:17 , GDP B:204 , HOH B:301 , HOH B:305 , HOH B:307 , HOH B:308	BINDING SITE FOR RESIDUE CA B 201
6	AC6	SOFTWARE	GLU B:63 , GLY B:138 , HOH B:314 , HOH B:325 , HOH B:326 , HOH B:350	BINDING SITE FOR RESIDUE CA B 202
7	AC7	SOFTWARE	GLY B:10 , CYS B:12 , ALA B:59 , GLY B:60 , GLN B:61 , ARG B:68 , TYR B:71 , MET B:72 , TYR B:96 , ILE B:100 , HOH B:329 , HOH B:332 , HOH B:410	BINDING SITE FOR RESIDUE 20H B 203
8	AC8	SOFTWARE	GLY B:13 , VAL B:14 , GLY B:15 , LYS B:16 , SER B:17 , ALA B:18 , PHE B:28 , ASP B:30 , ASN B:116 , LYS B:117 , ASP B:119 , LEU B:120 , SER B:145 , ALA B:146 , LYS B:147 , CA B:201 , HOH B:301 , HOH B:307 , HOH B:345 , HOH B:346 , HOH B:348 , HOH B:375 , HOH B:387 , HOH B:401 , HOH B:408	BINDING SITE FOR RESIDUE GDP B 204

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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:168
                                                                                                                                                                                                        
               SCOP domains d4lv6a_ A: automated matches                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhhhhhhhh...........eeeeeeeee..eeeeeeeee.......hhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhh......eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lv6 A   1 MTEYKLVVVGACGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETSLLDILDTAGQEEYSAMRDQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKE 168
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain B from PDB  Type:PROTEIN  Length:167
                                                                                                                                                                                                       
               SCOP domains d4lv6b_ B: automated matches                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhhhhhhhh...........eeeeeeeee..eeeeeeeee.......hhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lv6 B   1 MTEYKLVVVGACGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETSLLDILDTAGQEEYSAMRDQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHK 167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (49, 49)

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	Ligands, Modified Residues, Ions
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	Sites
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Biological Units
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