6EN5

Crystal structure A of the Angiotensin-1 converting enzyme N-domain in complex with a diprolyl inhibitor.

PDB DOI: https://doi.org/10.2210/pdb6EN5/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2017-10-04 Released: 2017-12-20
Deposition Author(s): Cozier, G.E., Acharya, K.R., Fienberg, S., Chibale, K., Sturrock, E.D.
Funding Organization(s): Medical Research Council (United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.198
R-Value Work: 0.173
R-Value Observed: 0.173

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 304.58 kDa
Atom Count: 23,529
Modelled Residue Count: 2,433
Deposited Residue Count: 2,516
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme	A, B, C, D	629	Homo sapiens	Mutation(s): 0 Gene Names: ACE, DCP, DCP1 EC: 3.2.1 (PDB Primary Data), 3.4.15.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P12821 (Homo sapiens) Explore P12821 Go to UniProtKB: P12821
PHAROS: P12821 GTEx: ENSG00000159640
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12821
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, H, K	2		N-Glycosylation	Interactions Focus chain E Focus chain H Focus chain K Interactions & Density Focus chain E Focus chain H Focus chain K
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	F, I	4		N-Glycosylation	Interactions Focus chain F Focus chain I Interactions & Density Focus chain F Focus chain I
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G, J, M, P	3		N-Glycosylation	Interactions Focus chain G Focus chain J Focus chain M Focus chain P Interactions & Density Focus chain G Focus chain J Focus chain M Focus chain P
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

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

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	O	6		N-Glycosylation	Interactions Focus chain O Interactions & Density Focus chain O
Glycosylation Resources
GlyTouCan: G82348BZ GlyCosmos: G82348BZ GlyGen: G82348BZ

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE3 Query on PE3 Download Ideal Coordinates CCD File SDF format, chain GA [auth A] MOL2 format, chain GA [auth A]	GA [auth A]	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL C₂₈ H₅₈ O₁₅ ILLKMACMBHTSHP-UHFFFAOYSA-N		Interactions Focus chain GA [auth A] Interactions & Density Focus chain GA [auth A]
XPE Query on XPE Download Ideal Coordinates CCD File SDF format, chain ZB [auth D] MOL2 format, chain ZB [auth D]	ZB [auth D]	3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL C₂₀ H₄₂ O₁₁ DTPCFIHYWYONMD-UHFFFAOYSA-N		Interactions Focus chain ZB [auth D] Interactions & Density Focus chain ZB [auth D]
BJ2 Query on BJ2 Download Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain ZA [auth C] SDF format, chain IA [auth B] SDF format, chain PB [auth D] MOL2 format, chain R [auth A] MOL2 format, chain ZA [auth C] MOL2 format, chain IA [auth B] MOL2 format, chain PB [auth D]	IA [auth B], PB [auth D], R [auth A], ZA [auth C]	(2~{S})-1-[(2~{S})-2-[[(1~{S})-1-[(2~{S})-1-[(2~{S})-2-azanyl-4-oxidanyl-4-oxidanylidene-butanoyl]pyrrolidin-2-yl]-2-oxidanyl-2-oxidanylidene-ethyl]amino]propanoyl]pyrrolidine-2-carboxylic acid C₁₈ H₂₈ N₄ O₈ AEFOOLCGQAWEBH-JNLQPACOSA-N		Interactions Focus chain IA [auth B] Focus chain PB [auth D] Focus chain R [auth A] Focus chain ZA [auth C] Interactions & Density Focus chain IA [auth B] Focus chain PB [auth D] Focus chain R [auth A] Focus chain ZA [auth C]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain NB [auth C] SDF format, chain XA [auth B] MOL2 format, chain NB [auth C] MOL2 format, chain XA [auth B]	NB [auth C], XA [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain NB [auth C] Focus chain XA [auth B] Interactions & Density Focus chain NB [auth C] Focus chain XA [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain WA [auth B] MOL2 format, chain WA [auth B]	WA [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain WA [auth B] Interactions & Density Focus chain WA [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain DB [auth C] SDF format, chain NA [auth B] SDF format, chain OA [auth B] SDF format, chain PA [auth B] SDF format, chain SB [auth D] SDF format, chain TB [auth D] SDF format, chain CB [auth C] SDF format, chain LA [auth B] SDF format, chain MA [auth B] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] MOL2 format, chain DB [auth C] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain SB [auth D] MOL2 format, chain TB [auth D] MOL2 format, chain CB [auth C] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A]	CB [auth C] DB [auth C] LA [auth B] MA [auth B] NA [auth B] CB [auth C], DB [auth C], LA [auth B], MA [auth B], NA [auth B], OA [auth B], PA [auth B], SB [auth D], TB [auth D], U [auth A], V [auth A], W [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain CB [auth C] Focus chain DB [auth C] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain SB [auth D] Focus chain TB [auth D] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Interactions & Density Focus chain CB [auth C] Focus chain DB [auth C] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain SB [auth D] Focus chain TB [auth D] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain OB [auth D] SDF format, chain Q [auth A] SDF format, chain YA [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain OB [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain YA [auth C]	HA [auth B], OB [auth D], Q [auth A], YA [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain HA [auth B] Focus chain OB [auth D] Focus chain Q [auth A] Focus chain YA [auth C] Interactions & Density Focus chain HA [auth B] Focus chain OB [auth D] Focus chain Q [auth A] Focus chain YA [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain DA [auth A] SDF format, chain GB [auth C] SDF format, chain HB [auth C] SDF format, chain IB [auth C] SDF format, chain LB [auth C] SDF format, chain QA [auth B] SDF format, chain RA [auth B] SDF format, chain TA [auth B] SDF format, chain UB [auth D] SDF format, chain WB [auth D] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] SDF format, chain CA [auth A] SDF format, chain EB [auth C] SDF format, chain FB [auth C] SDF format, chain JB [auth C] SDF format, chain KB [auth C] SDF format, chain SA [auth B] SDF format, chain UA [auth B] SDF format, chain VB [auth D] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain GB [auth C] MOL2 format, chain HB [auth C] MOL2 format, chain IB [auth C] MOL2 format, chain LB [auth C] MOL2 format, chain QA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain UB [auth D] MOL2 format, chain WB [auth D] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain EB [auth C] MOL2 format, chain FB [auth C] MOL2 format, chain JB [auth C] MOL2 format, chain KB [auth C] MOL2 format, chain SA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain VB [auth D]	AA [auth A] BA [auth A] CA [auth A] DA [auth A] EB [auth C] AA [auth A], BA [auth A], CA [auth A], DA [auth A], EB [auth C], FB [auth C], GB [auth C], HB [auth C], IB [auth C], JB [auth C], KB [auth C], LB [auth C], QA [auth B], RA [auth B], SA [auth B], TA [auth B], UA [auth B], UB [auth D], VB [auth D], WB [auth D], 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 BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HB [auth C] Focus chain IB [auth C] Focus chain JB [auth C] Focus chain KB [auth C] Focus chain LB [auth C] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain UB [auth D] Focus chain VB [auth D] Focus chain WB [auth D] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HB [auth C] Focus chain IB [auth C] Focus chain JB [auth C] Focus chain KB [auth C] Focus chain LB [auth C] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain UB [auth D] Focus chain VB [auth D] Focus chain WB [auth D] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain EA [auth A] SDF format, chain MB [auth C] SDF format, chain XB [auth D] SDF format, chain YB [auth D] SDF format, chain FA [auth A] SDF format, chain VA [auth B] MOL2 format, chain EA [auth A] MOL2 format, chain MB [auth C] MOL2 format, chain XB [auth D] MOL2 format, chain YB [auth D] MOL2 format, chain FA [auth A] MOL2 format, chain VA [auth B]	EA [auth A] FA [auth A] MB [auth C] VA [auth B] XB [auth D] EA [auth A], FA [auth A], MB [auth C], VA [auth B], XB [auth D], YB [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain EA [auth A] Focus chain FA [auth A] Focus chain MB [auth C] Focus chain VA [auth B] Focus chain XB [auth D] Focus chain YB [auth D] Interactions & Density Focus chain EA [auth A] Focus chain FA [auth A] Focus chain MB [auth C] Focus chain VA [auth B] Focus chain XB [auth D] Focus chain YB [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain S [auth A] SDF format, chain JA [auth B] SDF format, chain QB [auth D] MOL2 format, chain AB [auth C] MOL2 format, chain S [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain QB [auth D]	AB [auth C], JA [auth B], QB [auth D], S [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AB [auth C] Focus chain JA [auth B] Focus chain QB [auth D] Focus chain S [auth A] Interactions & Density Focus chain AB [auth C] Focus chain JA [auth B] Focus chain QB [auth D] Focus chain S [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain BB [auth C] SDF format, chain KA [auth B] SDF format, chain RB [auth D] MOL2 format, chain T [auth A] MOL2 format, chain BB [auth C] MOL2 format, chain KA [auth B] MOL2 format, chain RB [auth D]	BB [auth C], KA [auth B], RB [auth D], T [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BB [auth C] Focus chain KA [auth B] Focus chain RB [auth D] Focus chain T [auth A] Interactions & Density Focus chain BB [auth C] Focus chain KA [auth B] Focus chain RB [auth D] Focus chain T [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
BJ2	Binding MOAD: 6EN5	Ki: 11.45 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.198
R-Value Work: 0.173
R-Value Observed: 0.173
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.167	α = 84.86
b = 103.447	β = 85.49
c = 115.446	γ = 81.99

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-12-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	MR/M026647/1

Revision History (Full details and data files)

Version 1.0: 2017-12-20
Type: Initial release
Version 1.1: 2018-01-24
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary