7P7P | pdb_00007p7p

Crystal structure of ERAP2 aminopeptidase in complex with phosphinic pseudotripeptide((1R)-1-Amino-3-phenylpropyl){(2S)-3-[((2S)-1-amino-1-oxo-3-phenylpropan-2-yl)amino]-2-{[3-(2-hydroxyphenyl)-isoxazol-5-yl]methyl}-3-oxopropyl}phosphinic acid

PDB DOI: https://doi.org/10.2210/pdb7P7P/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2021-07-20 Released: 2022-01-26
Deposition Author(s): Giastas, P., Stratikos, E., Mpakali, A.
Funding Organization(s): European Union (EU)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.231 (Depositor), 0.230 (DCC)
R-Value Work:
0.180 (Depositor), 0.182 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Inhibitor-Dependent Usage of the S1' Specificity Pocket of ER Aminopeptidase 2.

Mpakali, A., Georgiadis, D., Stratikos, E., Giastas, P.

(2022) ACS Med Chem Lett 13: 218-224

PubMed: 35178178 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.1c00582
Primary Citation Related Structures:
7P7P, 7PFS

PubMed Abstract:
Endoplasmic reticulum aminopeptidase 2 (ERAP2) is an intracellular enzyme involved in the processing of antigenic peptides intended for presentation by major histocompatibility complex class I (MHCI) molecules. Because of its role in regulating immune responses, ERAP2 is an emerging pharmacological target. Phosphinic pseudopeptides are potent transition-state analogue inhibitors of ERAP2. Previous structure-activity studies have revealed a complex but ambiguous relationship between the occupation of putative specificity pockets and the inhibitor efficacy. To address these problems, we solved crystal structures of ERAP2 in complex with two phosphinic pseudotripeptide inhibitors. Both compounds are found in the catalytic site in a canonical orientation for transition-state analogues and utilize the S1 and S2' pockets in a similar fashion. Strikingly, their P1' side chains exhibit different orientations and make interactions with distinct shallow pockets near the ERAP2 active site. These structures suggest that S1' pocket usage in ERAP2 may be inhibitor-dependent and constitute useful starting templates for the further optimization of this class of compounds.

Organizational Affiliation

National Centre for Scientific Research Demokritos, Agia Paraskevi, Athens 15341, Greece.

Macromolecule Content

Total Structure Weight: 230.75 kDa
Atom Count: 14,914
Modeled Residue Count: 1,782
Deposited Residue Count: 1,924
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoplasmic reticulum aminopeptidase 2	A, B	962	Homo sapiens	Mutation(s): 1 Gene Names: ERAP2, LRAP EC: 3.4.11
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P179 (Homo sapiens) Explore Q6P179 Go to UniProtKB: Q6P179
PHAROS: Q6P179 GTEx: ENSG00000164308
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6P179
Glycosylation
Glycosylation Sites: 9	Glycosylation Focus chain A Focus chain B	Go to GlyGen: Q6P179-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	4		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	4		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, H, I	2		N-Glycosylation	Interactions Focus chain E Focus chain H Focus chain I Interactions & Density Focus chain E Focus chain H Focus chain I
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	3		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	5		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
62S Query on 62S Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain CA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain CA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain CA [auth B]	CA [auth B], J [auth A]	[(2~{S})-3-[[(2~{S})-1-azanyl-1-oxidanylidene-3-phenyl-propan-2-yl]amino]-2-[[3-(2-hydroxyphenyl)-1,2-oxazol-5-yl]methyl]-3-oxidanylidene-propyl]-[(1~{R})-1-azanyl-3-phenyl-propyl]phosphinic acid C₃₁ H₃₅ N₄ O₆ P GSWUIYHGTPVQDP-FNHKZSGOSA-N		Interactions Focus chain CA [auth B] Focus chain J [auth A] Interactions & Density Focus chain CA [auth B] Focus chain J [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain L [auth A] SDF format, chain GA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain L [auth A] MOL2 format, chain GA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain L [auth A] mmCIF format, chain GA [auth B]	DA [auth B] EA [auth B] FA [auth B] GA [auth B] HA [auth B] DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], IA [auth B], K [auth A], L [auth A], M [auth A], N [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain R [auth A] MOL2 format, chain R [auth A] mmCIF format, chain R [auth A]	R [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Interactions & Density Focus chain R [auth A]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain Q [auth A]	Q [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A]	O [auth A], P [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain O [auth A] Focus chain P [auth A]
PDO Query on PDO Download:Ideal Coordinates CCD File SDF format, chain U [auth A] SDF format, chain JA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain JA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain JA [auth B]	JA [auth B], U [auth A]	1,3-PROPANDIOL C₃ H₈ O₂ YPFDHNVEDLHUCE-UHFFFAOYSA-N		Interactions Focus chain JA [auth B] Focus chain U [auth A] Interactions & Density Focus chain JA [auth B] Focus chain U [auth A]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain W [auth A] MOL2 format, chain W [auth A] mmCIF format, chain W [auth A]	W [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain W [auth A] Interactions & Density Focus chain W [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain KA [auth B] SDF format, chain BA [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain BA [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain BA [auth A]	BA [auth A], KA [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain KA [auth B] Interactions & Density Focus chain BA [auth A] Focus chain KA [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] SDF format, chain V [auth A] SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain AA [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain V [auth A] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain V [auth A] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain AA [auth A]	AA [auth A] S [auth A] T [auth A] V [auth A] X [auth A] AA [auth A], S [auth A], T [auth A], V [auth A], X [auth A], Y [auth A], Z [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain V [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain V [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]