4BVD

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free: 0.214
R-Value Work: 0.176
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08519
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BU6 Query on BU6 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	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		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free: 0.214
R-Value Work: 0.176
R-Value Observed: 0.177
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-07-16

Deposition Author(s):

Svalstedt Karlsson, B.

Revision History (Full details and data files)

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

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Help and Resources

4BVD

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

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)