4PNC

E. COLI METHIONINE AMINOPEPTIDASE IN COMPLEX WITH INHIBITOR 7-METHOXY-2-METHYLEN-3,4-DIHYDRONAPHTHALEN-1(2H)-ONE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.134 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Beta-aminoketones as prodrugs for selective irreversible inhibitors of type-1 methionine aminopeptidases.

Altmeyer, M.Amtmann, E.Heyl, C.Marschner, A.Scheidig, A.J.Klein, C.D.

(2014) Bioorg Med Chem Lett 24: 5310-5314

  • DOI: 10.1016/j.bmcl.2014.09.047
  • Primary Citation of Related Structures:  
    4PNC

  • PubMed Abstract: 
  • We identified and characterized β-aminoketones as prodrugs for irreversible MetAP inhibitors that are selective for the MetAP-1 subtype. β-Aminoketones with certain structural features form α,β-unsaturated ketones under physiological conditions, which bind covalently and selectively to cysteines in the S1 pocket of MetAP-1 ...

    We identified and characterized β-aminoketones as prodrugs for irreversible MetAP inhibitors that are selective for the MetAP-1 subtype. β-Aminoketones with certain structural features form α,β-unsaturated ketones under physiological conditions, which bind covalently and selectively to cysteines in the S1 pocket of MetAP-1. The binding mode was confirmed by X-ray crystallography and assays with the MetAPs from Escherichia coli, Staphylococcus aureus and both human isoforms. The initially identified tetralone derivatives showed complete selectivity for E. coli MetAP versus human MetAP-1 and MetAP-2. Rational design of indanone analogs yielded compounds with selectivity for the human type-1 versus the human type-2 MetAP.


    Organizational Affiliation

    Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology, IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany. Electronic address: c.klein@uni-heidelberg.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Methionine aminopeptidaseA264Escherichia coliMutation(s): 1 
Gene Names: 
mapBN17_45901BU34_07510ECs0170LF82_1274map_1map_2map_3A5U30_000305A6519_003665A6583_16595A6592_03000A8499_001873A8C65_17855A8W81_000034A9819_00780A9X72_20420AAG43_001514ABE90_007040ACN002_0172ACN68_08325ACN81_28550ACU57_18580ADS93_001965AM270_18155AM340_01180AM464_17635AML23_20680APX88_24815AT335_002550AT845_002207AUQ29_01565AW059_09830AW086_02695AZZ83_003979B6R12_000947B6R15_000229B6R17_000034B6R27_000726B6R48_000726B6R87_000727B9T59_07530BANRA_00641BANRA_01126BANRA_02274BANRA_03338BB545_20885BE930_13695BE963_14820BF271_001566BF481_003690BFL24_00925BG821_001277BG944_001873BH692_11600BHF52_16820BHS81_00635BHS87_00790BIQ87_00780BIZ41_19090BJI68_15635BJJ90_21365BK272_10845BK292_13665BK373_09590BK375_04650BM922_001353BMC34_001126BMC79_000034BMT49_02170BMT50_04015BMT91_01370BO068_002858BOH76_17730BON63_15460BON65_09420BON66_02965BON70_27140BON72_09365BON73_05305BON76_15455BON86_04400BON87_26705BON91_06970BON92_02740BON93_03950BON94_19490BON95_13045BON96_17225BON98_18195BOY03_001164BR158_000501BTQ06_06475BUE81_01720BUE82_19990BvCms2454_04108BvCmsC61A_04363BvCmsHHP019_00045BvCmsHHP056_04095BvCmsKKP036_03789BvCmsKKP057_02470BvCmsKKP061_01636BvCmsKSNP073_05553BvCmsKSP011_02199BvCmsKSP067_02027BvCmsKSP076_03013BvCmsNSNP036_02486BvCmsSIP024_03995BvCmsSIP082_04441BVL39_02200BWI89_14065BXT93_00695BZL69_20215C2121_002935C4952_002844C4M78_19950C5542_002028C5715_17360C5F72_21635C5N07_08565C5Y87_12560C6B13_04335C6B22_09345C6L19_002513C7B02_09170C9114_07030C9160_13590C9E67_25220C9Z43_09520C9Z62_06965CA593_02880CCS08_22600CCV12_002001CD42_002698CDC27_24680CDL36_07895CDL37_07235CDL57_02245CF32_003769CG692_09510CG831_000821CIG67_16565CN875_001362CO706_23040COD50_18610CQP61_22095CR539_04925CT143_22130CV83915_01408CWS33_09605CXJ73_002502D0X26_09430D2183_03900D3822_17345D3G36_16670D3O91_03175D3Y67_16395D4U49_05960D4V09_07025D5H22_06000D6T60_04055D9D31_08880D9D77_16615D9E34_01110D9E49_02150D9F92_13890D9H13_16240D9H94_14030D9J11_16820D9J61_11505DAH18_22150DAH23_11210DAH34_04200DAH37_16345DAH50_07070DB282_22015DD762_01080DEN89_20270DEN95_12150DEO15_08435DL654_15700DLW88_03765DLX40_11070DM968_04655DN627_10255DNQ45_10125DNX30_02280DP258_09365DRW19_04940DS732_05760DS966_12915DTL43_05935DTL90_09725DTM10_02770DTM45_12620DU321_03645DXB10_06655DXT69_01485DXT71_01895E0I42_18975E0N24_06875E0P28_15445E2112_01245E2119_15575E2123_14995E2127_15005E2128_01345E2129_02865E2135_11630E3N34_09350E4K51_05795E4K54_08045E5P52_06845E5S34_18375E5S35_00175E5S38_07595E5S43_01805E5S47_12315E5S52_09540E5S61_20150E5S62_13860EA239_13425EA435_20385EAI46_03650EAN77_17430EAX79_05565EBP16_09110EC1094V2_3685EC3234A_2c01490EC95NR1_04352EGC08_05785EH88_001885EHD79_10740EHH55_16990EI021_19840EI041_03165EIA08_06320EIA13_13545EIZ93_07930EL79_3706EL80_3653ELT17_01245ELT21_15040ELT31_08690ELT33_15875ELT48_12175ELT49_18470ELT58_11810ELT72_19815ELU83_06365ELU85_21275ELU95_07265ELV08_10285ELV10_05880ELV13_13140ELV22_16450ELV24_19205ELX56_19470ELX68_15970ELX69_11250ELX70_19400ELX76_14545ELX79_12495ELX83_20610ELY05_11465ELY23_06770ELY24_11285ELY50_16145EO241_11795EQO00_21090ERS085358_03259ERS085366_02717ERS085386_01545ERS085406_00567ERS139208_01226Esc0902E_01680ETECE1373_03889ETECE36_04792ETECE925_03852EVY14_15610EWK56_14880ExPECSC038_03991EXX13_05310EXX79_00175EYX47_12825EYX55_12760EYY34_22890F2N27_19275F2N28_19550F2N31_00170F3N40_16015F6U69_20635F7F11_02080F9386_00175F9571_18165F9S76_22060F9S83_02280F9V24_09495FC554_18130FDM60_08825FE587_16365FEJ01_15055FFF58_06190FGG80_07190FHD44_14145FHR00_00175FJQ51_00175FKO60_12345FMP09_04930FNJ67_21470FOI11_012845FOI11_22835FPI65_00920FPS82_06125FQF29_01535FV293_02900FVB16_04530FWK02_17915FY127_02950FZN30_04790G3565_18160G3813_000516G4A38_19335G5632_13940G5696_01305G6P89_20365G6Z99_21815G9448_10120GAJ26_21375GF147_13285GF646_01385GF699_14265GFY34_15720GFY48_19080GFZ60_03500GIB53_10115GKF52_14720GKF86_01185GKF89_14785GKG12_02125GKZ24_00175GLW94_14805GNO40_01335GNZ05_09830GOP20_16750GP650_06510GP662_15460GP711_09525GP946_16425GP979_07870GQA06_13080GQE64_01400GQF58_20340GQF59_21010GQM04_19835GQM09_07085GQM10_19895GQW07_00975GQW68_00175GQW76_10570GQW80_13510GRC73_19585GRO95_02770GRW05_07690GRW57_10415GRW80_16655GRW81_09805GTP88_05410GUB08_19155GUB92_12150GUC01_17875GUI33_00170GW978_09655GXU05_001403GXV26_001259H4P47_19645H4P50_20640H4P51_20490H5C78_04190HH411_000481HH795_000801HHG09_000092HHH44_003664HI055_000777HIE29_003102HIE44_000372HIN64_000551HIR12_003082HIT56_004088HJM92_002759HJQ60_000693HJS41_003084HJU54_003403HKA49_001653HL425_05500HL601_07695HLU10_19955HLU56_21425HLV18_20620HLZ20_18040HLZ50_06965HmCms169_00359HMJ82_00175HMS79_09970HMU06_10060HMU48_04760HMV41_18165HMV95_04590HMW38_10580HNC30_00175HNC36_16155HNC38_19265HNC52_16425HNC59_20340HNC66_11690HNC75_04080HNC99_17420HND12_10350HND24_07515HNV65_08980HNV94_05405HNY50_06350HNY54_07085HVV39_17625HVV53_21495HVW04_10230HVW11_05985HVW43_11760HVX16_21160HVX31_16120HVY77_20970HVZ30_16750HVZ33_19755HVZ71_20405HX136_20605HZ72_000284I6H00_14090I6H01_17690I6H02_18645JE86ST02C_01620JE86ST05C_01650MJ49_06200MS7163_00185NCTC10082_01385NCTC10089_04078NCTC10090_02162NCTC10418_06080NCTC10974_04618NCTC11022_04892NCTC11112_03431NCTC11126_03632NCTC11181_01364NCTC11341_03643NCTC12950_04426NCTC13127_05457NCTC13216_02712NCTC4450_07401NCTC7927_04509NCTC7928_04611NCTC8008_03675NCTC8009_07324NCTC8179_01375NCTC8500_04548NCTC8621_04204NCTC8959_04841NCTC8960_01564NCTC8985_03116NCTC9001_05427NCTC9036_04026NCTC9044_03182NCTC9048_04436NCTC9073_03396NCTC9111_04267NCTC9117_05055NCTC9434_02608NCTC9702_04762NCTC9703_03437NCTC9775_02330NCTC9777_00474NCTC9969_04267ND22_002550PGD_03808PU06_23045RG28_03915SAMEA3472043_02524SAMEA3472044_04159SAMEA3472056_00975SAMEA3472064_04386SAMEA3472080_03750SAMEA3472112_04655SAMEA3472117_04736SAMEA3472120_03163SAMEA3484427_01373SAMEA3484429_01108SAMEA3485101_01104SAMEA3485110_03714SAMEA3751407_04816SAMEA3752312_01945SAMEA3752386_04704SAMEA3752557_00872SAMEA3753064_03368SAMEA3753290_00391SAMEA3753300_01865THOESC010_36710TUM18780_36040WP2S18E08_37760WP4S18E07_36960WP4S18E08_36610WQ89_09550WR15_02325

EC: 3.4.11.18
UniProt
Find proteins for C3TPN7 (Escherichia coli)
Explore C3TPN7 
Go to UniProtKB:  C3TPN7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC3TPN7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7NP
Query on 7NP

Download Ideal Coordinates CCD File 
B [auth A](2S)-7-methoxy-2-methyl-3,4-dihydronaphthalen-1(2H)-one
C12 H14 O2
YVPRDJIRFPVNJW-QMMMGPOBSA-N
 Ligand Interaction
CO
Query on CO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.134 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.01α = 90
b = 66.82β = 111.15
c = 48.45γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
XDSdata scaling
XSCALEdata scaling
Cootmodel building
HKL2Mapmodel building
SHELXCDphasing
ARP/wARPmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Deutsche KrebshilfeGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2014-11-05
    Changes: Database references
  • Version 1.2: 2014-12-10
    Changes: Database references
  • Version 1.3: 2015-02-04
    Changes: Derived calculations
  • Version 1.4: 2017-09-27
    Changes: Advisory, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.5: 2019-11-20
    Changes: Derived calculations, Refinement description