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(-) Description

Title :  MENIN IN COMPLEX WITH MI-503
 
Authors :  J. Pollock, D. Borkin, T. Cierpicki, J. Grembecka
Date :  06 Dec 14  (Deposition) - 15 Apr 15  (Release) - 29 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.59
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Binding-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Borkin, S. He, H. Miao, K. Kempinska, J. Pollock, J. Chase, T. Purohit, B. Malik, T. Zhao, J. Wang, B. Wen, H. Zong, M. Jones, G. Danet-Desnoyers, M. L. Guzman, M. Talpaz, D. L. Bixby, D. Sun, J. L. Hess, A. G. Muntean, I. Maillard, T. Cierpicki, J. Grembecka
Pharmacologic Inhibition Of The Menin-Mll Interaction Block Progression Of Mll Leukemia In Vivo.
Cancer Cell V. 27 589 2015
PubMed-ID: 25817203  |  Reference-DOI: 10.1016/J.CCELL.2015.02.016

(-) Compounds

Molecule 1 - MENIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-459;
UNP RESIDUES 537-593
    Gene: MEN1, SCG2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 10)

Asymmetric/Biological Unit (6, 10)
No.NameCountTypeFull Name
13XW1Ligand/Ion4-METHYL-1-(1H-PYRAZOL-4-YLMETHYL)-5-[(4-{[6-(2,2,2-TRIFLUOROETHYL)THIENO[2,3-D]PYRIMIDIN-4-YL]AMINO}PIPERIDIN-1-YL)METHYL]-1H-INDOLE-2-CARBONITRILE
2DMS3Ligand/IonDIMETHYL SULFOXIDE
3EDO1Ligand/Ion1,2-ETHANEDIOL
4EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
5PG41Ligand/IonTETRAETHYLENE GLYCOL
6SO43Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:155 , LEU A:177 , SER A:178 , ASP A:180 , HIS A:181 , ALA A:182 , PHE A:238 , TYR A:276 , MET A:278 , MET A:322 , TYR A:323 , TRP A:341 , GLU A:363 , GLU A:366 , VAL A:371 , DMS A:602 , HOH A:806 , HOH A:822 , HOH A:823 , HOH A:948binding site for residue 3XW A 601
02AC2SOFTWARE3XW A:601 , HOH A:827 , HOH A:828binding site for residue DMS A 602
03AC3SOFTWARELEU A:75 , THR A:76 , TYR A:361 , PHE A:365 , HOH A:708 , HOH A:711 , HOH A:870 , HOH A:1009binding site for residue PG4 A 603
04AC4SOFTWAREPRO A:12 , ARG A:14 , HOH A:973binding site for residue SO4 A 604
05AC5SOFTWARETYR A:133 , PHE A:134 , ARG A:137 , ARG A:332binding site for residue SO4 A 605
06AC6SOFTWARELYS A:377 , ARG A:446binding site for residue SO4 A 606
07AC7SOFTWAREPHE A:43 , PHE A:47 , GLN A:400 , HOH A:885 , HOH A:895binding site for residue DMS A 607
08AC8SOFTWAREVAL A:185 , GLY A:190 , GLU A:191 , TYR A:227 , ARG A:229 , SER A:583binding site for residue DMS A 608
09AC9SOFTWARETRP A:126 , LYS A:135binding site for residue 04E A 609
10AD1SOFTWAREVAL A:50 , ASN A:331 , ARG A:332 , VAL A:334 , ARG A:335 , GLY A:401 , ALA A:403binding site for residue EPE A 610

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4X5Y)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:2 -Leu A:3
2Phe A:11 -Pro A:12

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4X5Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4X5Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4X5Y)

(-) Sequences/Alignments

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:468
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhh.....hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhh............hhhhhhhhh..hhhhhhhhhhhhhhhh.....eeee....eeeeehhhhheee................hhhhhhh.hhhhhhhh.ee.hhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhh..ee....ee...hhhhhhhhhhhh....hhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4x5y A   2 GLKAAQKTLFPLRSIDDVVRLFAAELGREEPDLVLLSLVLGFVEHFLAVNRVGLTYFPVADLSIIAALYARFTAQIRGAVDLSLYPREGGVSSRELVKKVSDVIWNSLSRSYFKDRAHIQSLFSFITGTKLDSSGVAFAVVGACQALGLRDVHLALSEDHAWVVFGPNGEQTAEVTWHGKGNEDRRGQTVNAGVAERSWLYLKGSYMRCDRKMEVAFMVCAINPSIDLHTDSLELLQLQQKLLWLLYDLGHLERYPMALGNLADLEELEPTPGRPDPLTLYHKGIASAKTYYRDEHIYPYMYLAGYHCRNRNVREALQAWADTATVIQDYNYCREDEEIYKEFFEVANDVIPNLLKEAASLLEAGSQGSALQDPECFAHLLRFYDGICKWEEGSPTPVLHVGWATFLVQSLGRFEGQVRQKVRIVSVPVLTFQSEKMKGMKELLVATKINSSAIKLQLTAQSQVQMKK 589
                                    11        21        31        41        51 ||     81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381    || 403       413       423       433       443       453      |551       561       571       581        
                                                                              53|                                                                                                                                                                                                                                                                                                                     386|                                                          460|                                        
                                                                               74                                                                                                                                                                                                                                                                                                                      399                                                           549
   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 4X5Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4X5Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4X5Y)

(-) Gene Ontology  (57, 57)

Asymmetric/Biological Unit(hide GO term definitions)

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  4x5y
    Family and Domain Information: ProDom | SYSTERS
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  MEN1_HUMAN | O00255
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 Related Entries

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

UniProtKB/Swiss-Prot
        MEN1_HUMAN | O00255: 3u84 3u85 3u86 3u88 4gpq 4gq3 4gq4 4gq6 4i80 4og3 4og4 4og5 4og6 4og7 4og8 4x5z 5db0 5db1 5db2 5db3 5dd9 5dda 5ddb 5ddc 5ddd 5dde 5ddf

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4X5Y)