6VGC

Crystal Structures of FLAP bound to DG-031

PDB DOI: https://doi.org/10.2210/pdb6VGC/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2020-01-07 Released: 2020-12-02
Deposition Author(s): Ho, J.D., Lee, M.R., Rauch, C.T., Aznavour, K., Park, J.S., Luz, J.G., Antonysamy, S., Condon, B., Maletic, M., Zhang, A., Hickey, M.J., Hughes, N.E., Chandrasekhar, S., Sloan, A.V., Gooding, K., Harvey, A., Yu, X.P., Kahl, S.D., Norman, B.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free: 0.285
R-Value Work: 0.254
R-Value Observed: 0.255

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

Literature

Structure-based, multi-targeted drug discovery approach to eicosanoid inhibition: Dual inhibitors of mPGES-1 and 5-lipoxygenase activating protein (FLAP).

Ho, J.D., Lee, M.R., Rauch, C.T., Aznavour, K., Park, J.S., Luz, J.G., Antonysamy, S., Condon, B., Maletic, M., Zhang, A., Hickey, M.J., Hughes, N.E., Chandrasekhar, S., Sloan, A.V., Gooding, K., Harvey, A., Yu, X.P., Kahl, S.D., Norman, B.H.

(2020) Biochim Biophys Acta Gen Subj 1865: 129800-129800

PubMed: 33246032 Search on PubMed
DOI: https://doi.org/10.1016/j.bbagen.2020.129800
Primary Citation of Related Structures:
6VGC, 6VGI, 6VL4

PubMed Abstract:
Due to the importance of both prostaglandins (PGs) and leukotrienes (LTs) as pro-inflammatory mediators, and the potential for eicosanoid shunting in the presence of pathway target inhibitors, we have investigated an approach to inhibiting the formation of both PGs and LTs as part of a multi-targeted drug discovery effort.

Organizational Affiliation

Lilly Biotechnology Center, San Diego, CA 92121, USA. Electronic address: ho_joseph_d@lilly.com.

Macromolecule Content

Total Structure Weight: 118.5 kDa
Atom Count: 7,340
Modelled Residue Count: 901
Deposited Residue Count: 1,026
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-lipoxygenase-activating protein	A, B, C, D, E A, B, C, D, E, F	171	Homo sapiens	Mutation(s): 0 Gene Names: ALOX5AP, FLAP Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P20292 (Homo sapiens) Explore P20292 Go to UniProtKB: P20292
PHAROS: P20292 GTEx: ENSG00000132965
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20292
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QY1 (Subject of Investigation/LOI) Query on QY1 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain K [auth D] SDF format, chain M [auth E] SDF format, chain N [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth D] MOL2 format, chain M [auth E] MOL2 format, chain N [auth F]	G [auth A] H [auth B] J [auth C] K [auth D] M [auth E] G [auth A], H [auth B], J [auth C], K [auth D], M [auth E], N [auth F]	(2R)-cyclopentyl{4-[(quinolin-2-yl)methoxy]phenyl}acetic acid C₂₃ H₂₃ N O₃ ZEYYDOLCHFETHQ-JOCHJYFZSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain M [auth E] Focus chain N [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain M [auth E] Focus chain N [auth F]
BOG Query on BOG Download Ideal Coordinates CCD File SDF format, chain O [auth F] MOL2 format, chain O [auth F]	O [auth F]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain O [auth F] Interactions & Density Focus chain O [auth F]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain L [auth D] MOL2 format, chain I [auth B] MOL2 format, chain L [auth D]	I [auth B], L [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain L [auth D] Interactions & Density Focus chain I [auth B] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free: 0.285
R-Value Work: 0.254
R-Value Observed: 0.255
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.911	α = 90
b = 101.488	β = 99.83
c = 111.864	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-12-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-12-02
Type: Initial release
Version 1.1: 2020-12-09
Changes: Database references
Version 1.2: 2020-12-16
Changes: Database references
Version 1.3: 2023-10-11
Changes: Data collection, Database references, Refinement description

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6VGC

Crystal Structures of FLAP bound to DG-031

Structure-based, multi-targeted drug discovery approach to eicosanoid inhibition: Dual inhibitors of mPGES-1 and 5-lipoxygenase activating protein (FLAP).

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)