6WY5
CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH Compound-37 A.K.A 7-(1-phenyl-3-(((1S,3S)-3-phenyl-2,3-dihydro-1H-inden-1-yl)amino)propyl)-1H-[1,2,3]triazolo[4,5-b]pyridin-5-amine
- PDB DOI: https://doi.org/10.2210/pdb6WY5/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Homo sapiens
- Mutation(s): No 
- Deposited: 2020-05-12 Released: 2020-10-14 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.90 Å
- R-Value Free: 0.245 
- R-Value Work: 0.222 
- R-Value Observed: 0.223 
This is version 1.2 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Myeloperoxidase light chain | A, C [auth D] | 105 | Homo sapiens | Mutation(s): 0  EC: 1.11.2.2 | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P05164 (Homo sapiens) Explore P05164  Go to UniProtKB:  P05164 | |||||
PHAROS:  P05164 GTEx:  ENSG00000005381  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P05164 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Myeloperoxidase heavy chain | B, D [auth E] | 467 | Homo sapiens | Mutation(s): 0  EC: 1.11.2.2 | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P05164 (Homo sapiens) Explore P05164  Go to UniProtKB:  P05164 | |||||
PHAROS:  P05164 GTEx:  ENSG00000005381  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P05164 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 3 | |||||
---|---|---|---|---|---|
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 [auth C], G | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 4 | |||||
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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 | F, H | 6 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G82348BZ GlyCosmos:  G82348BZ GlyGen:  G82348BZ |
Small Molecules
Ligands 5 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
HEC Query on HEC | I [auth A], N [auth D] | HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N | |||
UF7 (Subject of Investigation/LOI) Query on UF7 | M [auth B], R [auth E] | 7-[(1R)-1-phenyl-3-{[(1S,3S)-3-phenyl-2,3-dihydro-1H-inden-1-yl]amino}propyl]-3H-[1,2,3]triazolo[4,5-b]pyridin-5-amine C29 H28 N6 PUZMDZNRNPQCRQ-DSBYRVASSA-N | |||
NAG Query on NAG | P [auth E] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
CA Query on CA | K [auth B], Q [auth E] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | |||
CL Query on CL | J [auth A], L [auth B], O [auth D] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
CSO Query on CSO | B, D [auth E] | L-PEPTIDE LINKING | C3 H7 N O3 S | CYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.90 Å
- R-Value Free: 0.245 
- R-Value Work: 0.222 
- R-Value Observed: 0.223 
- Space Group: P 43 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 107.902 | α = 90 |
b = 107.902 | β = 90 |
c = 240.141 | γ = 90 |
Software Name | Purpose |
---|---|
BUSTER | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2020-10-14  Deposition Author(s): Khan, J.A.
Revision History (Full details and data files)
- Version 1.0: 2020-10-14
Type: Initial release - Version 1.1: 2023-10-18
Changes: Advisory, Data collection, Database references, Refinement description - Version 1.2: 2023-11-15
Changes: Data collection