4BVD | pdb_00004bvd

Identification of small molecule inhibitors selective for apo(a) kringles KIV-7, KIV-10 and KV.

• PDB DOI: https://doi.org/10.2210/pdb4BVD/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2013-06-25 Released: 2014-07-16 
• Deposition Author(s): Sandmark, J., Althage, M., Andersson, G.M.K., Antonsson, T., Blaho, S., Bodin, C., Bostrom, J., Chen, Y., Dahlen, A., Eriksson, P.O., Evertsson, E., Fex, T., Fjellstrom, O., Gustafsson, D., Hallberg, C., Hicks, R., Jarkvist, E., Johansson, C., Kalies, I., Kang, D., Svalstedt Karlsson, B., Kartberg, F., Legnehed, A., Lindqvist, A.M., Martinsson, S.A., Moberg, A., Petersson, A.U., Ridderstrom, M., Thelin, A., Tigerstrom, A., Vinblad, J., Xu, B., Knecht, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 
  0.214 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Small Molecules Used to Decipher the Pathophysiological Roles of the Kringle Domains Kiv-7, - 10 and Kv of Apolipoprotein(A)

Sandmark, J., Althage, M., Andersson, G.M.K., Antonsson, T., Blaho, S., Bodin, C., Bostrom, J., Chen, Y., Dahlen, A., Eriksson, P.O., Evertsson, E., Fex, T., Fjellstrom, O., Gustafsson, D., Hallberg, C., Hicks, R., Jarkvist, E., Johansson, C., Kalies, I., Kang, D., Svalstedt Karlsson, B., Kartberg, F., Legnehed, A., Lindqvist, A.M., Martinsson, S.A., Moberg, A., Petersson, A.U., Ridderstrom, M., Thelin, A., Tigerstrom, A., Vinblad, J., Xu, B., Knecht, W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 9.55 kDa 
• Atom Count: 769 
• Modeled Residue Count: 78 
• Deposited Residue Count: 79 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
APOLIPOPROTEIN(A)	A	79	Homo sapiens	Mutation(s): 1  EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08519 (Homo sapiens) Explore P08519  Go to UniProtKB:  P08519
PHAROS:  P08519 GTEx:  ENSG00000198670

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BU6	C [auth A]	5-chloro-2-fluoro-N-[1-(4-piperidyl)pyrazol-4-yl]benzenesulfonamide C14 H16 Cl F N4 O2 S XMUAZEINLRUFHP-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free:  0.214 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.24	α = 90
b = 45.27	β = 90
c = 58.12	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-16 
Deposition Author(s): Sandmark, J., Althage, M., Andersson, G.M.K., Antonsson, T., Blaho, S., Bodin, C., Bostrom, J., Chen, Y., Dahlen, A., Eriksson, P.O., Evertsson, E., Fex, T., Fjellstrom, O., Gustafsson, D., Hallberg, C., Hicks, R., Jarkvist, E., Johansson, C., Kalies, I., Kang, D., Svalstedt Karlsson, B., Kartberg, F., Legnehed, A., Lindqvist, A.M., Martinsson, S.A., Moberg, A., Petersson, A.U., Ridderstrom, M., Thelin, A., Tigerstrom, A., Vinblad, J., Xu, B., Knecht, W.

Revision History  

• Version 1.0: 2014-07-16
  Type: Initial release
  
• Version 1.1: 2018-04-04
  Changes: Data collection
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary