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(-) Description

Title :  DISCOVERY OF POTENT MCL-1 INHIBITORS USING FRAGMENT-BASED METHODS AND STRUCTURE-BASED DESIGN
 
Authors :  A. Friberg, B. Zhao
Date :  07 Nov 12  (Deposition) - 09 Jan 13  (Release) - 06 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.53
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Anti-Apoptotic Protein, Bh3 Peptides, Apoptosis (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

(-) Compounds

Molecule 1 - INDUCED MYELOID LEUKEMIA CELL DIFFERENTIATION PROTEIN MCL- 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    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
 
Molecule 2 - MCL-1 BH3 PEPTIDE
    Chains: C, D
    Engineered: YES
    Other Details: SYNTHETIC PEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2NH22Mod. Amino AcidAMINO GROUP
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2NH21Mod. Amino AcidAMINO GROUP
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2NH21Mod. Amino AcidAMINO GROUP

(-) Sites  (0, 0)

(no "Site" information available for 4HW4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HW4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4HW4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HW4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HW4)

(-) Exons   (0, 0)

(no "Exon" information available for 4HW4)

(-) 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:154
                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hw4 A 171 GDELYRQSLEIISRYLREQATGAKDTKPMGRSGATSRKALETLRRVGDGVQRNHETAFQGMLRKLDIKNEDDVKSLSRVMIHVFSDGVTNWGRIVTLISFGAFVAKHLKTINQESCIEPLAESITDVLVRTKRDWLVKQRGWDGFVEFFHVEDL 324
                                   180       190       200       210       220       230       240       250       260       270       280       290       300       310       320    


Chain B from PDB  Type:PROTEIN  Length:141
                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hw4 B 171 GDELYRQSLEIISRYLREQATGGATSRKALETLRRVGDGVQRNHETAFQGMLRKLDIKNEDDVKSLSRVMIHVFSDGVTNWGRIVTLISFGAFVAKHLKTINQESCIEPLAESITDVLVRTKRDWLVKQRGWDGFVEFFHV 321
                                   180       190 ||    210       220       230       240       250       260       270       280       290       300       310       320 
                                               192|                                                                                                                      
                                                203                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:18
                                                  
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
                 Transcript ------------------ Transcript
                 4hw4 C   0 xALETLRRVGDGVQRNHx  17
                            |        9       |
                            0-ACE           17-NH2


Chain D from PDB  Type:PROTEIN  Length:18
                                                  
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
                 Transcript ------------------ Transcript
                 4hw4 D   0 xALETLRRVGDGVQRNHx  17
                            |        9       |
                            |               17-NH2
                            0-ACE
   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)

(no "SCOP Domain" information available for 4HW4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HW4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HW4)

(-) Gene Ontology  (32, 32)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MCL1_HUMAN | Q07820: 2kbw 2mhs 2nl9 2nla 2pqk 3d7v 3io9 3kj0 3kj1 3kj2 3kz0 3mk8 3pk1 3twu 3wix 3wiy 4bpi 4bpj 4hw2 4hw3 4oq5 4oq6 4wgi 4wmr 4wms 4wmt 4wmu 4wmv 4wmw 4wmx 4zbf 4zbi 5c3f 5c6h 5fc4 5fdo 5fdr 5iez 5if4 5jsb 5ku9 5lof 5mes 5mev 5uum 5vkc

(-) Related Entries Specified in the PDB File

4hw2 4hw3 4hw4