4CPT - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   MACROCYCLIC TRANSITION-STATE MIMICKING HIV-1 PROTEASE INHIBITORS ENCOMPASSING A TERTIARY ALCOHOL

Authors :   M. Derosa, J. Unge, H. V. Motwani, A. Rosenquist, L. Vrang, H. Wallberg,

Date :   08 Feb 14 (Deposition) - 17 Dec 14 (Release) - 17 Dec 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A,B

Keywords :   Hydrolase, Hiv-1 Protease, Inhibitor, Rational Drug Design, Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. De Rosa, J. Unge, H. V. Motwani, A. Rosenquist, L. Vrang, H. Wallberg, M. Larhed
Synthesis Of P1'-Functionalized Macrocyclic Transition- State Mimicking Hiv-1 Protease Inhibitors Encompassing A Tertiary Alcohol.
J. Med. Chem. V. 57 6444 2014
PubMed-ID: 25054811 | Reference-DOI: 10.1021/JM500434Q

Molecule 1 - PROTEASE
	Atcc	:	11676
	Chains	:	A, B
	EC Number	:	3.4.23.16
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PEXP5
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Variant	:	AI
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	HUMAN IMMUNODEFICIENCY VIRUS
	Organism Taxid	:	12721
	Strain	:	99HHP1 (D10)
	Synonym	:	PR, RETROPEPSIN
	Variant	:	Z2/CDC-Z34 ISOLATE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	1T8	1	Ligand/Ion	METHYL [(2S)-1-(2-{3-[(3R,6S,10Z)-3-HYDROXY-4,7-DIOXO-6-(PROPAN-2-YL)-5,8-DIAZABICYCLO[11.2.2]HEPTADECA-1(15),10,13,16-TETRAEN-3PROPYL}-2-[4-(PYRIDIN-3-YL)BENZYL]HYDRAZINYL)-3,3-DIMETHYL-1-OXOBUTAN-2-YL]CARBAMATE
2	CL	3	Ligand/Ion	CHLORIDE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP B:106 , HOH B:2091	BINDING SITE FOR RESIDUE CL B1200
2	AC2	SOFTWARE	THR A:74 , ASN A:88 , HOH A:2127 , ARG B:141	BINDING SITE FOR RESIDUE CL A1100
3	AC3	SOFTWARE	THR B:174 , ASN B:188 , HOH B:2106	BINDING SITE FOR RESIDUE CL B1201
4	AC4	SOFTWARE	ARG A:8 , ASP A:25 , GLY A:27 , ALA A:28 , ASP A:29 , GLY A:48 , GLY A:49 , PRO A:81 , THR A:82 , HOH A:2092 , ARG B:108 , LEU B:123 , ASP B:125 , GLY B:127 , ALA B:128 , ASP B:129 , GLY B:148 , GLY B:149 , PHE B:153 , HOH B:2084	BINDING SITE FOR RESIDUE 1T8 B1202

(no "SS Bond" information available for 4CPT)

(no "Cis Peptide Bond" information available for 4CPT)

(no "SAP(SNP)/Variant" information available for 4CPT)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASP_PROT_RETROV	PS50175	Aspartyl protease, retroviral-type family profile.	POL_HV1B1	520-589	2	A:20-89 B:120-189
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	POL_HV1B1	522-533	2	A:22-33 B:122-133

(no "Exon" information available for 4CPT)

Asymmetric/Biological 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:99
                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee..................eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 4cpt A   1 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPTPTNVIGRNLLTQIGCTLNF  99
                                    10        20        30        40        50        60        70        80        90

Chain B from PDB  Type:PROTEIN  Length:99
                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee..................eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 4cpt B 101 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPTPTNVIGRNLLTQIGCTLNF 199
                                   110       120       130       140       150       160       170       180       190

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 '\|'

(no "SCOP Domain" information available for 4CPT)

(no "CATH Domain" information available for 4CPT)

(no "Pfam Domain" information available for 4CPT)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological 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
		1T8	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4cpt)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	4cpt
		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
	POL_HV1B1 \| P03366
		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)
	3.4.23.16
		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

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	POL_HV1B1 \| P03366
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

4cpq	MACROCYCLIC TRANSITION-STATE MIMICKING HIV-1 PROTEASE INHIBITORS ENCOMPASSING A TERTIARY ALCOHOL
4cpr	MACROCYCLIC TRANSITION-STATE MIMICKING HIV-1 PROTEASE INHIBITORS ENCOMPASSING A TERTIARY ALCOHOL
4cps	MACROCYCLIC TRANSITION-STATE MIMICKING HIV-1 PROTEASE INHIBITORS ENCOMPASSING A TERTIARY ALCOHOL
4cpu	MACROCYCLIC TRANSITION-STATE MIMICKING HIV-1 PROTEASE INHIBITORS ENCOMPASSING A TERTIARY ALCOHOL
4cpw	MACROCYCLIC TRANSITION-STATE MIMICKING HIV-1 PROTEASE INHIBITORS ENCOMPASSING A TERTIARY ALCOHOL
4cpx	MACROCYCLIC TRANSITION-STATE MIMICKING HIV-1 PROTEASE INHIBITORS ENCOMPASSING A TERTIARY ALCOHOL

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (45, 45)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File