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(-) Description

Title :  MENIN IN COMPLEX WITH MI-352
 
Authors :  J. Pollock, B. Dmitry, T. Cierpicki, J. Grembecka
Date :  20 Aug 15  (Deposition) - 30 Mar 16  (Release) - 30 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Binding, Protein Binding-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Borkin, J. Pollock, K. Kempinska, T. Purohit, X. Li, B. Wen, T. Zhao, H. Miao, S. Shukla, M. He, D. Sun, T. Cierpicki, J. Grembecka
Property Focused Structure-Based Optimization Of Small Molecule Inhibitors Of The Protein-Protein Interaction Between Menin And Mixed Lineage Leukemia (Mll).
J. Med. Chem. V. 59 892 2016
PubMed-ID: 26744767  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01305

(-) Compounds

Molecule 1 - MENIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-459, 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  (5, 13)

Asymmetric/Biological Unit (5, 13)
No.NameCountTypeFull Name
158P1Ligand/Ion1-[(2S)-2,3-DIHYDROXYPROPYL]-5-[(4-{[6-(2,2,2-TRIFLUOROETHYL)THIENO[2,3-D]PYRIMIDIN-4-YL]AMINO}PIPERIDIN-1-YL)METHYL]-1H-INDOLE-2-CARBONITRILE
26E61Ligand/Ion1-[(2R)-2,3-DIHYDROXYPROPYL]-5-[(4-{[6-(2,2,2-TRIFLUOROETHYL)THIENO[2,3-D]PYRIMIDIN-4-YL]AMINO}PIPERIDIN-1-YL)METHYL]-1H-INDOLE-2-CARBONITRILE
3DMS4Ligand/IonDIMETHYL SULFOXIDE
4PG43Ligand/IonTETRAETHYLENE GLYCOL
5SO44Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:75 , THR A:76 , TYR A:361 , PHE A:365 , HOH A:707 , HOH A:846 , HOH A:864binding site for residue PG4 A 601
02AC2SOFTWAREPRO A:12 , ARG A:14 , HOH A:804binding site for residue SO4 A 602
03AC3SOFTWARETYR A:133 , PHE A:134 , ARG A:137 , LYS A:151binding site for residue SO4 A 603
04AC4SOFTWAREARG A:332 , VAL A:334 , ARG A:335 , GLY A:401 , ALA A:403 , HOH A:734 , HOH A:1046binding site for residue SO4 A 604
05AC5SOFTWARELYS A:377 , ARG A:446 , HOH A:957binding site for residue SO4 A 605
06AC6SOFTWAREPHE A:47 , GLY A:386 , GLN A:400 , HOH A:793 , HOH A:932 , HOH A:1029binding site for residue DMS A 606
07AC7SOFTWAREVAL A:185 , GLY A:190 , GLU A:191 , TYR A:227 , ARG A:229 , SER A:583binding site for residue DMS A 607
08AC8SOFTWARELYS A:135 , TRP A:198binding site for residue PG4 A 608
09AC9SOFTWARESER A:155 , 58P A:610 , 6E6 A:612 , DMS A:613 , HOH A:716binding site for residue DMS A 609
10AD1SOFTWARESER 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 , TYR A:319 , MET A:322 , TYR A:323 , GLY A:326 , TRP A:341 , GLU A:363 , GLU A:366 , DMS A:609 , 6E6 A:612 , DMS A:613 , HOH A:709 , HOH A:729 , HOH A:870 , HOH A:926 , HOH A:1010binding site for residue 58P A 610
11AD2SOFTWARETYR A:268 , ASP A:269 , GLY A:271 , GLU A:274 , HOH A:728binding site for residue PG4 A 611
12AD3SOFTWARESER 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 , TYR A:319 , MET A:322 , TYR A:323 , GLY A:326 , TRP A:341 , GLU A:363 , GLU A:366 , DMS A:609 , 58P A:610 , DMS A:613 , HOH A:709 , HOH A:870 , HOH A:926binding site for residue 6E6 A 612
13AD4SOFTWARESER A:155 , PHE A:238 , CYS A:241 , ALA A:242 , DMS A:609 , 58P A:610 , 6E6 A:612 , HOH A:716binding site for residue DMS A 613

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DB0)

(-) 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 5DB0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DB0)

(-) Exons   (0, 0)

(no "Exon" information available for 5DB0)

(-) 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.......hhhhhhhhhhhhhhh.............hhhhhhhhh..hhhhhhhhhhhhhhhh.....eeee....eeeeehhhhheee................hhhhhhh.hhhhhhhh.ee.hhhhhhhhhhhh...eee..eehhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhh..ee....ee...hhhhhhhhhhh.....hhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5db0 A   2 GLKAAQKTLFPLRSIDDVVRLFAAELGREEPDLVLLSLVLGFVEHFLAVNRVGLTYFPVADLSIIAALYARFTAQIRGAVDLSLYPREGGVSSRELVKKVSDVIWNSLSRSYFKDRAHIQSLFSFITGTKLDSSGVAFAVVGACQALGLRDVHLALSEDHAWVVFGPNGEQTAEVTWHGKGNEDRRGQTVNAGVAERSWLYLKGSYMRCDRKMEVAFMVCAINPSIDLHTDSLELLQLQQKLLWLLYDLGHLERYPMALGNLADLEELEPTPGRPDPLTLYHKGIASAKTYYRDEHIYPYMYLAGYHCRNRNVREALQAWADTATVIQDYNYCREDEEIYKEFFEVANDVIPNLLKEAASLLEAGSQGSALQDPECFAHLLRFYDGICKWEEGSPTPVLHVGWATFLVQSLGRFEGQVRQKVRIVSGPVLTFQSEKMKGMKELLVATKINSSAIKLQLTAQSQVQMKK 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|                                                         459|                                         
                                                                               74                                                                                                                                                                                                                                                                                                                      399                                                          548
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 5DB0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DB0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DB0)

(-) Gene Ontology  (57, 57)

Asymmetric/Biological Unit(hide GO term definitions)

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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 4x5y 4x5z 5db1 5db2 5db3 5dd9 5dda 5ddb 5ddc 5ddd 5dde 5ddf

(-) Related Entries Specified in the PDB File

5db1 5db2 5db3