4HW2 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 3 (Jmol Viewer)

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Biological Unit 5 (Jmol Viewer)

Biological Unit 6 (Jmol Viewer)

Title :   DISCOVERY OF POTENT MCL-1 INHIBITORS USING FRAGMENT-BASED METHODS AND STRUCTURE-BASED DESIGN

Authors :   B. Zhao

Date :   07 Nov 12 (Deposition) - 09 Jan 13 (Release) - 06 Mar 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: E  (1x)
Biol. Unit 6: F  (1x)

Keywords :   Regulation Of Apoptosis, Maintenance Of Viability, Apoptosis, Apoptosis-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Friberg, D. Vigil, B. Zhao, R. N. Daniels, J. P. Burke, P. M. Garcia-Barrantes, D. Camper, B. A. Chauder, T. Lee, E. T. Olejniczak, S. W. Fesik
Discovery Of Potent Myeloid Cell Leukemia 1 (Mcl-1) Inhibitors Using Fragment-Based Methods And Structure-Based Design.
J. Med. Chem. V. 56 15 2013
PubMed-ID: 23244564 | Reference-DOI: 10.1021/JM301448P

Molecule 1 - INDUCED MYELOID LEUKEMIA CELL DIFFERENTIATION PROTEIN MCL- 1
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDEST-HISMBP
	Expression System Strain	:	BL21-CODONPLUS (DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MCL1, BCL2L3
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	BCL-2-LIKE PROTEIN 3, BCL2-L-3, BCL-2-RELATED PROTEIN EAT/MCL1, MCL1/EAT

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D
Biological Unit 5 (1x)	:					E
Biological Unit 6 (1x)	:						F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 10)

No.	Name	Count	Type	Full Name
1	19H	6	Ligand/Ion	6-CHLORO-3-[3-(4-CHLORO-3,5-DIMETHYLPHENOXY)PROPYL]-1H-INDOLE-2-CARBOXYLIC ACID
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	PGE	3	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	19H	1	Ligand/Ion	6-CHLORO-3-[3-(4-CHLORO-3,5-DIMETHYLPHENOXY)PROPYL]-1H-INDOLE-2-CARBOXYLIC ACID
2	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
3	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	19H	1	Ligand/Ion	6-CHLORO-3-[3-(4-CHLORO-3,5-DIMETHYLPHENOXY)PROPYL]-1H-INDOLE-2-CARBOXYLIC ACID
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	PGE	2	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	19H	1	Ligand/Ion	6-CHLORO-3-[3-(4-CHLORO-3,5-DIMETHYLPHENOXY)PROPYL]-1H-INDOLE-2-CARBOXYLIC ACID
2	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
3	PGE	-1	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	19H	1	Ligand/Ion	6-CHLORO-3-[3-(4-CHLORO-3,5-DIMETHYLPHENOXY)PROPYL]-1H-INDOLE-2-CARBOXYLIC ACID
2	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
3	PGE	-1	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 5 (1, 1)

No.	Name	Count	Type	Full Name
1	19H	1	Ligand/Ion	6-CHLORO-3-[3-(4-CHLORO-3,5-DIMETHYLPHENOXY)PROPYL]-1H-INDOLE-2-CARBOXYLIC ACID
2	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
3	PGE	-1	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 6 (1, 1)

No.	Name	Count	Type	Full Name
1	19H	1	Ligand/Ion	6-CHLORO-3-[3-(4-CHLORO-3,5-DIMETHYLPHENOXY)PROPYL]-1H-INDOLE-2-CARBOXYLIC ACID
2	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
3	PGE	-1	Ligand/Ion	TRIETHYLENE GLYCOL

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:227 , PHE A:228 , VAL A:249 , MET A:250 , VAL A:253 , PHE A:254 , ARG A:263 , LEU A:267 , PHE A:270 , GLY A:271 , ILE A:294	BINDING SITE FOR RESIDUE 19H A 401
02	AC2	SOFTWARE	HIS A:224	BINDING SITE FOR RESIDUE PGE A 402
03	AC3	SOFTWARE	ALA B:227 , PHE B:228 , MET B:250 , VAL B:253 , PHE B:254 , ARG B:263 , LEU B:267 , PHE B:270	BINDING SITE FOR RESIDUE 19H B 401
04	AC4	SOFTWARE	HIS B:224 , THR B:266	BINDING SITE FOR RESIDUE PGE B 402
05	AC5	SOFTWARE	ASN B:223 , HIS B:224 , GLY B:262 , PHE B:318	BINDING SITE FOR RESIDUE PGE B 403
06	AC6	SOFTWARE	ASN B:223 , HIS B:224 , THR B:226 , ALA B:227	BINDING SITE FOR RESIDUE EDO B 404
07	AC7	SOFTWARE	ALA C:227 , PHE C:228 , MET C:231 , VAL C:253 , PHE C:254 , ARG C:263 , LEU C:267 , PHE C:270 , GLY C:271	BINDING SITE FOR RESIDUE 19H C 400
08	AC8	SOFTWARE	PHE D:228 , MET D:231 , LEU D:246 , VAL D:253 , PHE D:254 , ARG D:263 , LEU D:267 , PHE D:270 , GLY D:271	BINDING SITE FOR RESIDUE 19H D 400
09	AC9	SOFTWARE	ALA E:227 , MET E:231 , LEU E:246 , MET E:250 , VAL E:253 , PHE E:254 , ARG E:263 , LEU E:267 , PHE E:270	BINDING SITE FOR RESIDUE 19H E 400
10	BC1	SOFTWARE	LYS E:194 , ARG E:207 , ALA F:227 , PHE F:228 , MET F:231 , MET F:250 , VAL F:253 , PHE F:254 , ARG F:263 , LEU F:267 , PHE F:270	BINDING SITE FOR RESIDUE 19H F 400

(no "SS Bond" information available for 4HW2)

Asymmetric Unit

No.	Residues
1	Ala B:193	-	Lys B:194
2	Ala D:193	-	Lys D:194

(no "SAP(SNP)/Variant" information available for 4HW2)

(no "PROSITE Motif" information available for 4HW2)

(no "Exon" information available for 4HW2)

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:149
                                                                                                                                                                                     
               SCOP domains d4hw2a_ A: automated matches                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hw2 A 171 GDELYRQSLEIISRYLREQATGAKDTKPMSGATSRKALETLRRVGDGVQRNHETAFQGMLRKLDIKNEDDVKSLSRVMIHVFSDGVTNWGRIVTLISFGAFVAKHLKTINQESCIEPLAESITDVLVRTKRDWLVKQRGWDGFVEFFHV 321
                                   180       190       202       212       222       232       242       252       262       272       282       292       302       312         
                                                      199|                                                                                                                       
                                                       202

Chain B from PDB  Type:PROTEIN  Length:151
                                                                                                                                                                                       
               SCOP domains d4hw2b_ B: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hw2 B 171 GDELYRQSLEIISRYLREQATGAKDTKPMGRSGATSRKALETLRRVGDGVQRNHETAFQGMLRKLDIKNEDDVKSLSRVMIHVFSDGVTNWGRIVTLISFGAFVAKHLKTINQESCIEPLAESITDVLVRTKRDWLVKQRGWDGFVEFFHV 321
                                   180       190       200       210       220       230       240       250       260       270       280       290       300       310       320

Chain C from PDB  Type:PROTEIN  Length:150
                                                                                                                                                                                      
               SCOP domains d4hw2c_ C: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hw2 C 171 GDELYRQSLEIISRYLREQATGAKDTKPMGRSGATSRKALETLRRVGDGVQRNHETAFQGMLRKLDIKNEDDVKSLSRVMIHVFSDGVTNWGRIVTLISFGAFVAKHLKTINQESCIEPLAESITDVLVRTKRDWLVKQRGWDGFVEFFH 320
                                   180       190       200       210       220       230       240       250       260       270       280       290       300       310       320

Chain D from PDB  Type:PROTEIN  Length:151
                                                                                                                                                                                       
               SCOP domains d4hw2d_ D: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hw2 D 171 GDELYRQSLEIISRYLREQATGAKDTKPMGRSGATSRKALETLRRVGDGVQRNHETAFQGMLRKLDIKNEDDVKSLSRVMIHVFSDGVTNWGRIVTLISFGAFVAKHLKTINQESCIEPLAESITDVLVRTKRDWLVKQRGWDGFVEFFHV 321
                                   180       190       200       210       220       230       240       250       260       270       280       290       300       310       320

Chain E from PDB  Type:PROTEIN  Length:151
                                                                                                                                                                                       
               SCOP domains d4hw2e_ E: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hw2 E 171 GDELYRQSLEIISRYLREQATGAKDTKPMGRSGATSRKALETLRRVGDGVQRNHETAFQGMLRKLDIKNEDDVKSLSRVMIHVFSDGVTNWGRIVTLISFGAFVAKHLKTINQESCIEPLAESITDVLVRTKRDWLVKQRGWDGFVEFFHV 321
                                   180       190       200       210       220       230       240       250       260       270       280       290       300       310       320

Chain F from PDB  Type:PROTEIN  Length:150
                                                                                                                                                                                      
               SCOP domains d4hw2f_ F: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hw2 F 171 GDELYRQSLEIISRYLREQATGAKDTKPMGRSGATSRKALETLRRVGDGVQRNHETAFQGMLRKLDIKNEDDVKSLSRVMIHVFSDGVTNWGRIVTLISFGAFVAKHLKTINQESCIEPLAESITDVLVRTKRDWLVKQRGWDGFVEFFH 320
                                   180       190       200       210       220       230       240       250       260       270       280       290       300       310       320

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Membrane and cell surface proteins and peptides (2046)

Fold: Toxins' membrane translocation domains (135)

Superfamily: Bcl-2 inhibitors of programmed cell death (113)

Family: Bcl-2 inhibitors of programmed cell death (102)

Protein domain: automated matches (33)

Human (Homo sapiens) [TaxId: 9606] (31)

1a	d4hw2a_	A:
1b	d4hw2b_	B:
1c	d4hw2c_	C:
1d	d4hw2d_	D:
1e	d4hw2e_	E:
1f	d4hw2f_	F:

(no "CATH Domain" information available for 4HW2)

(no "Pfam Domain" information available for 4HW2)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Ala B:193 - Lys B:194	[ RasMol ]
		Ala D:193 - Lys D:194	[ RasMol ]

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	4hw2
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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