J. Y. Yin, Z. Chen, N. X. You, F. C. Li, H. Y. Zhang, J. Xue, H. Ma, Q. W. Zhao, L. S. Yu*, S. Zeng* & F. Zhu*. VARIDT 3.0: the phenotypic and regulatory variability of drug transporter. Nucleic Acids Research. 52(D1): D1490-D1502 (2024). PMID: 37819041
T. T. Fu, F. C. Li, Y. Zhang, J. Y. Yin, W. Q. Qiu, X. D. Li, X. G. Liu, W. W. Xin, C. Z. Wang, L. S. Yu, J. Q. Gao, Q. C. Zheng*, S. Zeng* & F. Zhu*. VARIDT 2.0: structural variability of drug transporter. Nucleic Acids Research. 50(D1): D1417-D1431 (2022). PMID: 34747471
J. Y. Yin, W. Sun, F. C. Li, J. J. Hong, X. X. Li, Y. Zhou, Y. J. Lu, M. Z. Liu, X. Zhang, N. Chen, X. P. Jin, J. Xue, S. Zeng*, L. S. Yu* & F. Zhu*. VARIDT 1.0: variability of drug transporter database. Nucleic Acids Research. 48(D1): D1042-D1450 (2020). PMID: 31495872
Current VARIDT Covered 424 Drug Transporters (DTs)/potential DTs Transporting 585 FDA Approved and 301 Clinical/Preclinical Drugs for 572 Diseases
Five Aspects of Phenotypic and Regulatory Variability are Provided for Each DT in VARIDT 3.0 (Graphic Illustration) :
α. Microbiota Influence (MBI) of DTs
2,072 MBI data of 145 DTs regulated by 124 microbe species, and the relative abundances of these microbe species across 76 diseases
β. Post-Translational Modification (PTM) of DTs
10,255 PTM data of 418 DTs that were related to 24 PTM types, and graphical illustrations on 9,717 experimentally-validated PTM sites
γ. Transcriptional Regulation (TSR) of DTs
10,610 TSR data of 381 DTs that were regulated by 357 TFs, and the differential expression profiles of these TFs across 59 organs and 106 diseases
δ. Epigenetic Regulation (EGR) of DTs
46,748 EGR data of 287 DTs related to 3 types of EGR
ε. Exogenous Modulation (EGM) of DTs
12,209 EGM data of 419 DTs modulated by 1,717 xenobiotics
Data Standardization in VARIDT 3.0 Facilitating Comprehensive Health Management :
1. Diseases Affected by the Drugs of Clinical Importance
All diseases were standardized using the latest version of International Classification of Diseases (ICD-11, released by the WHO)
2. Functional Family of Each Drug Transporter (DT)
Functional family of each DT was standardized using the phylogenetic classification of Transporter Classification Database (TCDB)
3. Unit of Kinetic Parameter (Km value) for Transporting Drugs
The affinity measured by Km value for the drugs transported by their corresponding DTs were unified to the unit of micromolar
4. 2D and 3D Structures of Small Molecular Drugs
The structures of the small molecular drugs transported by DTs were drawn and were standardized in the .sdf format (both 2D and 3D)
5. Crosslinking with Other Biological/Pharmaceutical Databases
UniProtKB, TCDB, dbSNP, Drugs@FDA, ClinicalTrials.gov, ICD-11, PubChem, ChEBI, TTD, NCBI Gene, CAS Registry Number, etc.
Four Aspects of Structural Variability are Provided for Each DT in VARIDT 2.0 (Graphic Illustration) :
α. Mutation-induced Spatial Variations in Folded State (MISVFS)
145 mutation-induced structures originating from 42 DTs
β. Difference among the DT Structures of Human and Model Organisms (DASHMO)
1,622 inter-species structures from 17 species covering 292 DTs
γ. Outward-facing and Inward-facing Conformations (OFAIFC)
118 conformations belonging to 59 DTs
δ. Xenobiotics-driven Alterations in 3D Complex (XEDAIC)
822 xenobiotics-regulated structures of 506 xenobiotics in complex with 57 DTs
Three Aspects of Genenal Variability Data are Provided for Each DT in VARIDT 1.0 (Graphic Illustration) :
α. Epigenetic Regulations and Genetic Polymorphisms of DTs (ERGPDT)
23,947 DNA methylations, 7,225 noncoding RNA regulations, 92 histone modifications and 1,278 genetic polymorphisms of DTs
β. Disease-, Species-, and Tissue-Specific Protein Abundances (DSTSPA)
Differential abundance profiles and downloadable data of 257 DTs in 21,781 patients/healthy individuals of 61 tissues and 108 diseases
Protein abundances of 245 DTs in 67 tissues of Homo sapiens or model organisms (Mus musculus and Rattus norvegicus)
γ. Exogenous Factors Modulating DT Activity (EFMDTA)
1,225 exogenous factors (dietary constituents, small molecular/biological drugs, natural products, etc.) modulating activity of 148 DTs
If you find any error in data or bug in web service, please kindly report it to Dr. Yin and Dr. Li.
