4X2T

X-ray crystal structure of the orally available aminopeptidase inhibitor, Tosedostat, bound to the M17 Leucyl Aminopeptidase from P. falciparum

PDB DOI: https://doi.org/10.2210/pdb4X2T/pdb

Classification: Hydrolase/Hydrolase Inhibitor
Organism(s): Plasmodium falciparum 3D7
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2014-11-27 Released: 2015-02-18
Deposition Author(s): Drinkwater, N., McGowan, S.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia), Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.73 Å
R-Value Free: 0.274
R-Value Work: 0.220
R-Value Observed: 0.223

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

X-ray crystal structures of an orally available aminopeptidase inhibitor, Tosedostat, bound to anti-malarial drug targets PfA-M1 and PfA-M17.

Drinkwater, N., Bamert, R.S., Sivaraman, K.K., Paiardini, A., McGowan, S.

(2015) Proteins 83: 789-795

PubMed: 25645579 Search on PubMed
DOI: https://doi.org/10.1002/prot.24771
Primary Citation of Related Structures:
4X2T, 4X2U

PubMed Abstract:
New anti-malarial treatments are desperately required to face the spread of drug resistant parasites. Inhibition of metalloaminopeptidases, PfA-M1 and PfA-M17, is a validated therapeutic strategy for treatment of Plasmodium falciparum malaria. Here, we describe the crystal structures of PfA-M1 and PfA-M17 bound to chemotherapeutic agent Tosedostat. The inhibitor occupies the enzymes' putative product egress channels in addition to the substrate binding pockets; however, adopts different binding poses when bound to PfA-M1 and PfA-M17. These findings will be valuable for the continued development of selective inhibitors of PfA-M1 and PfA-M17.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, 3800, Australia.

Macromolecule Content

Total Structure Weight: 700.42 kDa
Atom Count: 48,055
Modelled Residue Count: 6,144
Deposited Residue Count: 6,228
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
M17 leucyl aminopeptidase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	519	Plasmodium falciparum 3D7	Mutation(s): 3 Gene Names: LAP, PF14_0439
UniProt
Find proteins for Q8IL11 (Plasmodium falciparum (isolate 3D7)) Explore Q8IL11 Go to UniProtKB: Q8IL11
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8IL11
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TOD Query on TOD Download Ideal Coordinates CCD File SDF format, chain AC [auth L] SDF format, chain CA [auth C] SDF format, chain NB [auth I] SDF format, chain O [auth A] SDF format, chain SB [auth J] SDF format, chain WA [auth F] SDF format, chain AB [auth G] SDF format, chain IB [auth H] SDF format, chain PA [auth E] SDF format, chain WB [auth K] SDF format, chain X [auth B] MOL2 format, chain AC [auth L] MOL2 format, chain CA [auth C] MOL2 format, chain NB [auth I] MOL2 format, chain O [auth A] MOL2 format, chain SB [auth J] MOL2 format, chain WA [auth F] MOL2 format, chain AB [auth G] MOL2 format, chain IB [auth H] MOL2 format, chain PA [auth E] MOL2 format, chain WB [auth K] MOL2 format, chain X [auth B]	AB [auth G] AC [auth L] CA [auth C] IB [auth H] NB [auth I] AB [auth G], AC [auth L], CA [auth C], IB [auth H], NB [auth I], O [auth A], PA [auth E], SB [auth J], WA [auth F], WB [auth K], X [auth B]	(2S)-({(2R)-2-[(1S)-1-hydroxy-2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoyl}amino)(phenyl)ethanoic acid C₁₆ H₂₂ N₂ O₆ FIVIXKOBUJPPEI-AGIUHOORSA-N		Interactions Focus chain AB [auth G] Focus chain AC [auth L] Focus chain CA [auth C] Focus chain IB [auth H] Focus chain NB [auth I] Focus chain O [auth A] Focus chain PA [auth E] Focus chain SB [auth J] Focus chain WA [auth F] Focus chain WB [auth K] Focus chain X [auth B] Interactions & Density Focus chain AB [auth G] Focus chain AC [auth L] Focus chain CA [auth C] Focus chain IB [auth H] Focus chain NB [auth I] Focus chain O [auth A] Focus chain PA [auth E] Focus chain SB [auth J] Focus chain WA [auth F] Focus chain WB [auth K] Focus chain X [auth B]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain EB [auth G] SDF format, chain FA [auth C] SDF format, chain FB [auth G] SDF format, chain GA [auth C] SDF format, chain KB [auth H] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain T [auth A] SDF format, chain Z [auth B] SDF format, chain TA [auth E] MOL2 format, chain EB [auth G] MOL2 format, chain FA [auth C] MOL2 format, chain FB [auth G] MOL2 format, chain GA [auth C] MOL2 format, chain KB [auth H] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain T [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain TA [auth E]	EB [auth G] FA [auth C] FB [auth G] GA [auth C] KB [auth H] EB [auth G], FA [auth C], FB [auth G], GA [auth C], KB [auth H], LA [auth D], MA [auth D], T [auth A], TA [auth E], Z [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain EB [auth G] Focus chain FA [auth C] Focus chain FB [auth G] Focus chain GA [auth C] Focus chain KB [auth H] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain T [auth A] Focus chain TA [auth E] Focus chain Z [auth B] Interactions & Density Focus chain EB [auth G] Focus chain FA [auth C] Focus chain FB [auth G] Focus chain GA [auth C] Focus chain KB [auth H] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain T [auth A] Focus chain TA [auth E] Focus chain Z [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain CB [auth G] SDF format, chain DB [auth G] SDF format, chain DC [auth L] SDF format, chain EA [auth C] SDF format, chain KA [auth D] SDF format, chain PB [auth I] SDF format, chain R [auth A] SDF format, chain RA [auth E] SDF format, chain S [auth A] SDF format, chain SA [auth E] SDF format, chain Y [auth B] SDF format, chain CC [auth L] SDF format, chain Q [auth A] MOL2 format, chain CB [auth G] MOL2 format, chain DB [auth G] MOL2 format, chain DC [auth L] MOL2 format, chain EA [auth C] MOL2 format, chain KA [auth D] MOL2 format, chain PB [auth I] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth E] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth E] MOL2 format, chain Y [auth B] MOL2 format, chain CC [auth L] MOL2 format, chain Q [auth A]	CB [auth G] CC [auth L] DB [auth G] DC [auth L] EA [auth C] CB [auth G], CC [auth L], DB [auth G], DC [auth L], EA [auth C], KA [auth D], PB [auth I], Q [auth A], R [auth A], RA [auth E], S [auth A], SA [auth E], Y [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CB [auth G] Focus chain CC [auth L] Focus chain DB [auth G] Focus chain DC [auth L] Focus chain EA [auth C] Focus chain KA [auth D] Focus chain PB [auth I] Focus chain Q [auth A] Focus chain R [auth A] Focus chain RA [auth E] Focus chain S [auth A] Focus chain SA [auth E] Focus chain Y [auth B] Interactions & Density Focus chain CB [auth G] Focus chain CC [auth L] Focus chain DB [auth G] Focus chain DC [auth L] Focus chain EA [auth C] Focus chain KA [auth D] Focus chain PB [auth I] Focus chain Q [auth A] Focus chain R [auth A] Focus chain RA [auth E] Focus chain S [auth A] Focus chain SA [auth E] Focus chain Y [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain GB [auth H] SDF format, chain HA [auth D] SDF format, chain HB [auth H] SDF format, chain IA [auth D] SDF format, chain LB [auth I] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain OA [auth E] SDF format, chain QB [auth J] SDF format, chain RB [auth J] SDF format, chain UA [auth F] SDF format, chain V [auth B] SDF format, chain VB [auth K] SDF format, chain W [auth B] SDF format, chain YA [auth G] SDF format, chain YB [auth L] SDF format, chain ZB [auth L] SDF format, chain AA [auth C] SDF format, chain MB [auth I] SDF format, chain NA [auth E] SDF format, chain UB [auth K] SDF format, chain VA [auth F] SDF format, chain ZA [auth G] MOL2 format, chain BA [auth C] MOL2 format, chain GB [auth H] MOL2 format, chain HA [auth D] MOL2 format, chain HB [auth H] MOL2 format, chain IA [auth D] MOL2 format, chain LB [auth I] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain QB [auth J] MOL2 format, chain RB [auth J] MOL2 format, chain UA [auth F] MOL2 format, chain V [auth B] MOL2 format, chain VB [auth K] MOL2 format, chain W [auth B] MOL2 format, chain YA [auth G] MOL2 format, chain YB [auth L] MOL2 format, chain ZB [auth L] MOL2 format, chain AA [auth C] MOL2 format, chain MB [auth I] MOL2 format, chain NA [auth E] MOL2 format, chain UB [auth K] MOL2 format, chain VA [auth F] MOL2 format, chain ZA [auth G]	AA [auth C] BA [auth C] GB [auth H] HA [auth D] HB [auth H] AA [auth C], BA [auth C], GB [auth H], HA [auth D], HB [auth H], IA [auth D], LB [auth I], M [auth A], MB [auth I], N [auth A], NA [auth E], OA [auth E], QB [auth J], RB [auth J], UA [auth F], UB [auth K], V [auth B], VA [auth F], VB [auth K], W [auth B], YA [auth G], YB [auth L], ZA [auth G], ZB [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain GB [auth H] Focus chain HA [auth D] Focus chain HB [auth H] Focus chain IA [auth D] Focus chain LB [auth I] Focus chain M [auth A] Focus chain MB [auth I] Focus chain N [auth A] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain QB [auth J] Focus chain RB [auth J] Focus chain UA [auth F] Focus chain UB [auth K] Focus chain V [auth B] Focus chain VA [auth F] Focus chain VB [auth K] Focus chain W [auth B] Focus chain YA [auth G] Focus chain YB [auth L] Focus chain ZA [auth G] Focus chain ZB [auth L] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain GB [auth H] Focus chain HA [auth D] Focus chain HB [auth H] Focus chain IA [auth D] Focus chain LB [auth I] Focus chain M [auth A] Focus chain MB [auth I] Focus chain N [auth A] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain QB [auth J] Focus chain RB [auth J] Focus chain UA [auth F] Focus chain UB [auth K] Focus chain V [auth B] Focus chain VA [auth F] Focus chain VB [auth K] Focus chain W [auth B] Focus chain YA [auth G] Focus chain YB [auth L] Focus chain ZA [auth G] Focus chain ZB [auth L]
CO3 Query on CO3 Download Ideal Coordinates CCD File SDF format, chain BB [auth G] SDF format, chain DA [auth C] SDF format, chain JA [auth D] SDF format, chain JB [auth H] SDF format, chain P [auth A] SDF format, chain QA [auth E] SDF format, chain TB [auth J] SDF format, chain U [auth B] SDF format, chain XA [auth F] SDF format, chain BC [auth L] SDF format, chain OB [auth I] SDF format, chain XB [auth K] MOL2 format, chain BB [auth G] MOL2 format, chain DA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain JB [auth H] MOL2 format, chain P [auth A] MOL2 format, chain QA [auth E] MOL2 format, chain TB [auth J] MOL2 format, chain U [auth B] MOL2 format, chain XA [auth F] MOL2 format, chain BC [auth L] MOL2 format, chain OB [auth I] MOL2 format, chain XB [auth K]	BB [auth G] BC [auth L] DA [auth C] JA [auth D] JB [auth H] BB [auth G], BC [auth L], DA [auth C], JA [auth D], JB [auth H], OB [auth I], P [auth A], QA [auth E], TB [auth J], U [auth B], XA [auth F], XB [auth K]	CARBONATE ION C O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-L		Interactions Focus chain BB [auth G] Focus chain BC [auth L] Focus chain DA [auth C] Focus chain JA [auth D] Focus chain JB [auth H] Focus chain OB [auth I] Focus chain P [auth A] Focus chain QA [auth E] Focus chain TB [auth J] Focus chain U [auth B] Focus chain XA [auth F] Focus chain XB [auth K] Interactions & Density Focus chain BB [auth G] Focus chain BC [auth L] Focus chain DA [auth C] Focus chain JA [auth D] Focus chain JB [auth H] Focus chain OB [auth I] Focus chain P [auth A] Focus chain QA [auth E] Focus chain TB [auth J] Focus chain U [auth B] Focus chain XA [auth F] Focus chain XB [auth K]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.73 Å
R-Value Free: 0.274
R-Value Work: 0.220
R-Value Observed: 0.223
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 173.715	α = 90
b = 176.698	β = 90
c = 223.977	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2015-02-18

Deposition Author(s):

Drinkwater, N.

McGowan, S.

Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	1063786
Australian Research Council (ARC)	Australia	FT100100690

Revision History (Full details and data files)

Version 1.0: 2015-02-18
Type: Initial release
Version 1.1: 2015-04-08
Changes: Database references
Version 1.2: 2017-09-20
Changes: Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy
Version 1.3: 2020-01-01
Changes: Author supporting evidence
Version 1.4: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description