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(-) Description

Title :  MCL-1 COMPLEXED WITH SMALL MOLECULE INHIBITOR
 
Authors :  B. Zhao
Date :  16 Dec 15  (Deposition) - 02 Mar 16  (Release) - 23 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Mcl-1, Inhibitor, Apoptosis-Apoptosis Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. F. Pelz, Z. Bian, B. Zhao, S. Shaw, J. C. Tarr, J. Belmar, C. Gregg, D. V. Camper, C. M. Goodwin, A. L. Arnold, J. L. Sensintaffar, A. Friberg, O. W. Rossanese, T. Lee, E. T. Olejniczak, S. W. Fesik
Discovery Of 2-Indole-Acylsulfonamide Myeloid Cell Leukemia 1 (Mcl-1) Inhibitors Using Fragment-Based Methods.
J. Med. Chem. V. 59 2054 2016
PubMed-ID: 26878343  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01660

(-) Compounds

Molecule 1 - INDUCED MYELOID LEUKEMIA CELL DIFFERENTIATION PROTEIN MCL- 1
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 172-320
    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

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
15X24Ligand/Ion3-[3-(4-CHLORANYL-3,5-DIMETHYL-PHENOXY)PROPYL]-~{N}-(PHENYLSULFONYL)-1~{H}-INDOLE-2-CARBOXAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
15X21Ligand/Ion3-[3-(4-CHLORANYL-3,5-DIMETHYL-PHENOXY)PROPYL]-~{N}-(PHENYLSULFONYL)-1~{H}-INDOLE-2-CARBOXAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
15X21Ligand/Ion3-[3-(4-CHLORANYL-3,5-DIMETHYL-PHENOXY)PROPYL]-~{N}-(PHENYLSULFONYL)-1~{H}-INDOLE-2-CARBOXAMIDE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
15X21Ligand/Ion3-[3-(4-CHLORANYL-3,5-DIMETHYL-PHENOXY)PROPYL]-~{N}-(PHENYLSULFONYL)-1~{H}-INDOLE-2-CARBOXAMIDE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
15X21Ligand/Ion3-[3-(4-CHLORANYL-3,5-DIMETHYL-PHENOXY)PROPYL]-~{N}-(PHENYLSULFONYL)-1~{H}-INDOLE-2-CARBOXAMIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:228 , MET A:231 , LEU A:246 , MET A:250 , VAL A:253 , ASN A:260 , GLY A:262 , ARG A:263 , THR A:266 , LEU A:267 , PHE A:270 , GLY A:271 , ILE A:294 , ASN B:223 , HIS B:224binding site for residue 5X2 A 400
2AC2SOFTWAREASN A:223 , HIS A:224 , PHE B:228 , MET B:231 , LEU B:246 , MET B:250 , ASN B:260 , GLY B:262 , ARG B:263 , THR B:266 , LEU B:267 , PHE B:270 , GLY B:271binding site for residue 5X2 B 400
3AC3SOFTWAREHIS C:224 , PHE C:228 , MET C:231 , MET C:250 , VAL C:253 , ARG C:263 , THR C:266 , LEU C:267 , PHE C:270 , GLY C:271binding site for residue 5X2 C 400
4AC4SOFTWAREALA D:227 , PHE D:228 , MET D:231 , LEU D:246 , VAL D:249 , MET D:250 , VAL D:253 , GLY D:262 , ARG D:263 , THR D:266 , LEU D:267 , PHE D:270 , GLY D:271binding site for residue 5X2 D 400

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ala A:193 -Lys A:194
2Ser B:202 -Gly B:203
3Gly B:257 -Val B:258

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FDO)

(-) 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:142
                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fdo A 171 GDELYRQSLEIISRYLREQATGAKGATSRKALETLRRVGDGVQRNHETAFQGMLRKLDIKNEDDVKSLSRVMIHVFSDGVTNWGRIVTLISFGAFVAKHLKTINQESCIEPLAESITDVLVRTKRDWLVKQRGWDGFVEFFH 320
                                   180       190   ||  208       218       228       238       248       258       268       278       288       298       308       318  
                                                 194|                                                                                                                     
                                                  203                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:150
                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5fdo B 171 GDELYRQSLEIISRYLREQATGAKDTKPMGRSGATSRKALETLRRVGDGVQRNHETAFQGMLRKLDIKNEDDVKSLSRVMIHVFSDGVTNWGRIVTLISFGAFVAKHLKTINQESCIEPLAESITDVLVRTKRDWLVKQRGWDGFVEFFH 320
                                   180       190       200       210       220       230       240       250       260       270       280       290       300       310       320


Chain C from PDB  Type:PROTEIN  Length:143
                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fdo C 171 GDELYRQSLEIISRYLREQATGAKDGATSRKALETLRRVGDGVQRNHETAFQGMLRKLDIKNEDDVKSLSRVMIHVFSDGVTNWGRIVTLISFGAFVAKHLKTINQESCIEPLAESITDVLVRTKRDWLVKQRGWDGFVEFFH 320
                                   180       190    || 207       217       227       237       247       257       267       277       287       297       307       317   
                                                  195|                                                                                                                     
                                                   203                                                                                                                     


Chain D from PDB  Type:PROTEIN  Length:137
                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fdo D 171 GDELYRQSLEIISRYLREQATGATSRKALETLRRVGDGVQRNHETAFQGMLRKLDIKNEDDVKSLSRVMIHVFSVTNWGRIVTLISFGAFVAKHLKTINQESCIEPLAESITDVLVRTKRDWLVKQRGWDGFVEFFH 320
                                   180       190||     211       221       231       241       251   ||  263       273       283       293       303       313       
                                              191|                                                 255|                                                              
                                               203                                                  258
   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 5FDO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 32)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:193 - Lys A:194   [ RasMol ]  
    Gly B:257 - Val B:258   [ RasMol ]  
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  5fdo
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  MCL1_HUMAN | Q07820
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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 5fdr 5iez 5if4 5jsb 5ku9 5lof 5mes 5mev 5uum 5vkc

(-) Related Entries Specified in the PDB File

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