PDBsum entry 1j4h

Isomerase

PDB id

1j4h

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Contents

			Protein chain

					107 a.a. *

			Ligands

					SUB

			Waters ×137

* Residue conservation analysis

PDB id:

1j4h

Links

Name:

Isomerase

Title:

Crystal structure analysis of the fkbp12 complexed with 000107 small molecule

Structure:

Fkbp12. Chain: a. Synonym: fk506-binding protein. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.80Å

R-factor:

0.203

R-free:

0.250

Authors:

P.Li,Y.Ding,L.Wang,B.Wu,C.Shu,S.Li,B.Shen,Z.Rao

Key ref:

F.Sun et al. (2003). Design and structure-based study of new potential FKBP12 inhibitors. Biophys J, 85, 3194-3201. PubMed id: 14581219

Date:

30-Sep-01

Release date:

03-Jun-03

PROCHECK

	Headers

	References

Protein chain

P62942 (FKB1A_HUMAN) - Peptidyl-prolyl cis-trans isomerase FKBP1A from Homo sapiens

Seq: Struc:					108 a.a. 107 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.5.2.1.8 - peptidylprolyl isomerase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

[protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0)

Peptidylproline (omega=180)	=	peptidylproline (omega=0)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

	Biophys J 85:3194-3201 (2003)
PubMed id: 14581219

Design and structure-based study of new potential FKBP12 inhibitors.
F.Sun, P.Li, Y.Ding, L.Wang, M.Bartlam, C.Shu, B.Shen, H.Jiang, S.Li, Z.Rao.

ABSTRACT

Based on the structure of FKBP12 complexed with FK506 or rapamycin, with computer-aided design, two neurotrophic ligands, (3R)-4-(p-Toluenesulfonyl)-1,4-thiazane-3-carboxylic acid-L-Leucine ethyl ester and (3R)-4-(p-Toluenesulfonyl)-1,4-thiazane-3-carboxylic acid-L-phenylalanine benzyl ester, were designed and synthesized. Fluorescence experiments were used to detect the binding affinity between FKBP12 and these two ligands. Complex structures of FKBP12 with these two ligands were obtained by x-ray crystallography. In comparing FKBP12-rapamycin complex and FKBP12-FK506 complex as well as FKBP12-GPI-1046 solution structure with these new complexes, significant volume and surface area effects and obvious contact changes were detected which are expected to cause their different binding energies-showing these two novel ligands will become more effective neuron regeneration drugs than GPI-1046, which is currently undergoing phase II clinical trail as a neurotrophic drug. Analysis of volume and surface area effects also gives a new clue for structure-based drug design.

Literature references that cite this PDB file's key reference

PubMed id

Reference

18004757

M.H.Cheng, R.D.Coalson, and M.Cascio (2008).
Molecular dynamics simulations of ethanol binding to the transmembrane domain of the glycine receptor: implications for the channel potentiation mechanism.

Proteins, 71, 972-981.

16838311

Y.Xu, and R.Wang (2006).
A computational analysis of the binding affinities of FKBP12 inhibitors using the MM-PB/SA method.

Proteins, 64, 1058-1068.

16262683

N.Ramachandran, D.N.Larson, P.R.Stark, E.Hainsworth, and J.LaBaer (2005).
Emerging tools for real-time label-free detection of interactions on functional protein microarrays.

FEBS J, 272, 5412-5425.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.