4BTX

Crystal structure of human vascular adhesion protein-1 in complex with pyridazinone inhibitors

• PDB DOI: https://doi.org/10.2210/pdb4BTX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2013-06-19 Released: 2013-12-18 
• Deposition Author(s): Bligt-Linden, E., Pihlavisto, M., Szatmari, I., Otwinowski, Z., Smith, D.J., Lazar, L., Fulop, F., Salminen, T.A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free: 0.237 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 167.58 kDa 
• Atom Count: 11,686 
• Modelled Residue Count: 1,415 
• Deposited Residue Count: 1,474 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MEMBRANE PRIMARY AMINE OXIDASE	A, B	737	Homo sapiens	Mutation(s): 0  EC: 1.4.3.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q16853 (Homo sapiens) Explore Q16853  Go to UniProtKB:  Q16853
PHAROS:  Q16853 GTEx:  ENSG00000131471

Oligosaccharides

Help

Entity ID: 2
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	C	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G62182OO GlyCosmos:  G62182OO GlyGen:  G62182OO

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WF8	K [auth A], T [auth B]	5-isopropylamino-2-phenyl-6-(1H-1,2,4-triazol-5-yl)-3(2H)-pyridazinone C15 H16 N6 O VZIFGHQBDGDZHH-UHFFFAOYSA-N
NAG	H [auth A], I [auth A], J [auth A], P [auth B], Q [auth B], R [auth B], S [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN	O [auth B]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
CU	E [auth A], L [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
CA	F [auth A], G [auth A], M [auth B], N [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPQ	A, B	L-PEPTIDE LINKING	C9 H9 N O5		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
WF8	PDBBind:  4BTX	Ki: 290 (nM) from 1 assay(s)
	BindingDB:  4BTX	Kd: 200 (nM) from 1 assay(s)
		IC50: 290 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free: 0.237 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 226.35	α = 90
b = 226.35	β = 90
c = 217.226	γ = 120

Software Package:

Software Name	Purpose
HKL	data reduction
HKL	data scaling
CCP4	phasing
MOLREP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-18 
Deposition Author(s): Bligt-Linden, E., Pihlavisto, M., Szatmari, I., Otwinowski, Z., Smith, D.J., Lazar, L., Fulop, F., Salminen, T.A.

Revision History  

• Version 1.0: 2013-12-18
  Type: Initial release
  
• Version 1.1: 2014-01-15
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2023-12-20
  Changes: Data collection, Database references, Refinement description, Structure summary