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(-) Description

Title :  CRYSTAL STRUCTURE OF MCL1
 
Authors :  A. D. Ferguson
Date :  13 Jul 16  (Deposition) - 11 Jan 17  (Release) - 01 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Inhibitor, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. W. Johannes, S. Bates, C. Beigie, M. A. Belmonte, J. Breen, S. Cao, P. A. Centrella, M. A. Clark, J. W. Cuozzo, C. E. Dumelin, A. D. Ferguson S. Habeshian, D. Hargreaves, C. Joubran, S. Kazmirski, A. D. Keefe, M. L. Lamb, H. Lan, Y. Li, H. Ma, S. Mlynarski, M. J. Packer, P. B. Rawlins D. W. Robbins, H. Shen, E. A. Sigel, H. H. Soutter, N. Su, D. M. Troast, H. Wang, K. F. Wickson, C. Wu, Y. Zhang, Q. Zhao, X. Zheng, A. W. Hird
Structure Based Design Of Non-Natural Peptidic Macrocyclic Mcl-1 Inhibitors.
Acs Med Chem Lett V. 8 239 2017
PubMed-ID: 28197319  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.6B00464

(-) Compounds

Molecule 1 - INDUCED MYELOID LEUKEMIA CELL DIFFERENTIATION PROTEIN MCL- 1
    Chains: A, B
    EC Number: 3.6.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MCL1, BCL2L3
    Organism Common: MOUSE, HUMAN
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606
    Synonym: BCL-2-LIKE PROTEIN 3,BCL2-L-3,BCL-2-RELATED PROTEIN EAT/MCL1,MCL1/EAT

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
16XJ2Ligand/Ion(3~{S})-3-AZANYL-4-(4-BROMOPHENYL)-~{N}-[(3~{S})-1-[2-[[(2~{R})-1-(3,4-DICHLOROPHENYL)-4-(METHYLAMINO)-4-OXIDANYLIDENE-BUTAN-2-YL]AMINO]-2-OXIDANYLIDENE-ETHYL]-2-OXIDANYLIDENE-4,5-DIHYDRO-3~{H}-1-BENZAZEPIN-3-YL]BUTANAMIDE
2NA1Ligand/IonSODIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
16XJ1Ligand/Ion(3~{S})-3-AZANYL-4-(4-BROMOPHENYL)-~{N}-[(3~{S})-1-[2-[[(2~{R})-1-(3,4-DICHLOROPHENYL)-4-(METHYLAMINO)-4-OXIDANYLIDENE-BUTAN-2-YL]AMINO]-2-OXIDANYLIDENE-ETHYL]-2-OXIDANYLIDENE-4,5-DIHYDRO-3~{H}-1-BENZAZEPIN-3-YL]BUTANAMIDE
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
16XJ1Ligand/Ion(3~{S})-3-AZANYL-4-(4-BROMOPHENYL)-~{N}-[(3~{S})-1-[2-[[(2~{R})-1-(3,4-DICHLOROPHENYL)-4-(METHYLAMINO)-4-OXIDANYLIDENE-BUTAN-2-YL]AMINO]-2-OXIDANYLIDENE-ETHYL]-2-OXIDANYLIDENE-4,5-DIHYDRO-3~{H}-1-BENZAZEPIN-3-YL]BUTANAMIDE
2NA-1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:240 , ASN A:282 , GLN A:283 , SER A:285 , HOH A:542binding site for residue NA A 401
2AC2SOFTWAREHIS A:224 , MET A:231 , VAL A:249 , MET A:250 , HIS A:252 , VAL A:253 , SER A:255 , ASP A:256 , ARG A:263 , THR A:266 , PHE A:270 , ARG A:310 , GLU A:317 , HOH A:505 , HOH A:516 , HOH A:528 , HOH A:535binding site for residue 6XJ A 402
3AC3SOFTWAREARG A:176 , HIS B:224 , MET B:231 , HIS B:252 , VAL B:253 , ARG B:263 , PHE B:270binding site for residue 6XJ B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KU9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5KU9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KU9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KU9)

(-) Exons   (0, 0)

(no "Exon" information available for 5KU9)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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   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 ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ku9 A 172 DDLYRQSLEIISRYLREQATGSKKPLGEAGAAGRRALETLRRVGDGVQRNHETAFQGMLRKLDIKNEDDVKSLSRVMIHVFSDGVTNWGRIVTLISFGAFVAKHLKTINQESCIEPLAESITDVLVRTKRDWLVKQRGWDGFVEFFHVE 322
                                   181       191  ||   203       213       223       233       243       253       263       273       283       293       303       313         
                                                194|                                                                                                                             
                                                 197                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ku9 B 173 DLYRQSLEIISRYLREQATGRRALETLRRVGDGVQRNHETAFQGMLRKLDIKNEDDVKSLSRVMIHVFSDGVTNWGRIVTLISFGAFVAKHLKTINQESCIEPLAESITDVLVRTKRDWLVKQRGWDGFVEFFHVE 322
                                   182       192|      216       226       236       246       256       266       276       286       296       306       316      
                                             192|                                                                                                                   
                                              207
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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  (0, 0)

(no "SCOP Domain" information available for 5KU9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KU9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KU9)

(-) Gene Ontology  (32, 60)

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  5ku9
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  MCL1_HUMAN | Q07820
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  MCL1_MOUSE | P97287
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  3.6.1.11
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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 4hw4 4oq5 4oq6 4wgi 4wmr 4wms 4wmt 4wmu 4wmv 4wmw 4wmx 4zbf 4zbi 5c3f 5c6h 5fc4 5fdo 5fdr 5iez 5if4 5jsb 5lof 5mes 5mev 5uum 5vkc
        MCL1_MOUSE | P97287: 1wsx 2jm6 2nl9 2nla 2roc 2rod 3d7v 3io9 4bpi 4bpj 4g35 5mes 5mev

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5KU9)