Citations in PubMed

Primary Citation PubMed: 23118231 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 3

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

  • 3 per page
  • 5 per page
  • 10 per page
  • view all
  • Publication Year
  • Ascending
  • Descending

Study on incompatibility of traditional chinese medicine: evidence from formula network, chemical space, and metabolism room.

(2013) Evid Based Complement Alternat Med 2013

PubMed: 24369478 | PubMedCentral: PMC3858019 | DOI: 10.1155/2013/352145

The crystal structures of these enzymes were collected from PDB, with the names and their PDB code as follows: CYP 1A1 (PDB code: 4I8V), CYP 1A2 (PDB code: 2HI4), CYP 1B1 (PDB code: 3PM0), CYP 2A6 (PD... code: 1Z10), CYP 2A13 (PDB code: 2PB5), CYP 2B4 (PDB code: 3TMZ), CYP 2B6 (PDB code: 3UA5), CYP 2C5 (PDB code: 1NR6), CYP 2C8 (PDB code: 2VN0), CYP 2C9 (PDB code: 1R9O), CYP 2C18 (PDB code: 2H6P), CYP 2C19 (PDB code: 4GQS), CYP 2D6 (PDB code: 3TDA), CYP 2E1 (PDB code: 3T3Z), and CYP 3A4 (PDB code: 3NXU).

Publication Year: 2013


Clinical oxidative stress during leprosy multidrug therapy: impact of dapsone oxidation.

(2014) PLoS One 9

PubMed: 24465659 | PubMedCentral: PMC3899049 | DOI: 10.1371/journal.pone.0085712

The structure of the human microsomal CYP2C19 (4GQS, resolution 2.87 Å) obtained from the crystallographic protein data bank (PDB) and used in the study of docking was resolved experimentally ... y X-ray crystallography [25] .

Publication Year: 2014


Estimation of the binding modes with important human cytochrome P450 enzymes, drug interaction potential, pharmacokinetics, and hepatotoxicity of ginger components using molecular docking, computational, and pharmacokinetic modeling studies.

(2015) Drug Des Devel Ther 9

PubMed: 25733806 | PubMedCentral: PMC4338259 | DOI: 10.2147/DDDT.S74669

Figure 4 Binding modes of main active components of ginger in human CYP2C19 (PDB code 4GQS).

Table 1 Interacting forces of main active components of ginger with human CYP1A2, 2C9, 2D6, 2C19, and 3A4 Compound CDCOKER interaction energy (CIE kcal/mol) H-bond number Residues involved in H-bond formation Charge interaction Residues involved in charge interaction π–π stacking Residues involved in π–π stacking CYP1A2 (PDB ID: 2HI4) 6-Gingerol 55.9802 0 / 0 / 0 / 8-Gingerol 60.0329 0 / 0 / 0 / 10-Gingerol 61.3568 1 H-Gly316 0 / 0 / 6-Shogaol 55.9354 0 / 0 / 1 Phe260 8-Shogaol 58.6712 0 / 0 / 1 Phe260 10-Shogaol 56.4091 0 / 0 / 0 / Ar-Curcumene 36.2667 0 / 0 / 0 / β-Bisabolene 35.991 0 / 0 / 0 / β-Sesquiphelandrene 31.8433 0 / 0 / 0 / 6-Gingerdione 59.0853 0 / 0 / 2 Phe226 Phe260 (−)-Zingiberene 36.363 0 / 0 / 0 / Methyl-6-isogingerol 51.232 1 H-Gly316 0 / 1 Phe226 CYP2C9 (PDB ID: 1OG2) 6-Gingerol 38.3346 3 H-Leu208 O-Gln214 O-Asn217 0 / 0 / 8-Gingerol 41.0866 1 H-Leu208 0 / 0 / 10-Gingerol 45.8869 1 H-Leu208 0 / 0 / 6-Shogaol 38.4989 2 H-Thr301 O-Thr301 0 / 0 / 8-Shogaol 40.3159 0 / 0 / 0 / 10-Shogaol 45.2874 0 / 0 / 0 / Ar-Curcumene 27.0167 0 / 0 / 0 / β-Bisabolene 24.3503 0 / 0 / 0 / β-Sesquiphelandrene 24.6193 0 / 0 / 0 / 6-Gingerdione 38.5734 1 O-Asn107 0 / 0 / (−)-Zingiberene 25.4757 0 / 0 / 0 / Methyl-6-isogingerol 39.2082 1 H-Asp293 0 / 0 / CYP2C19 (PDB ID: 4GQS) 6-Gingerol 30.5894 1 H-Gly296 0 / 0 / 8-Gingerol 34.7882 1 O-Asn204 0 / 0 / 10-Gingerol 41.7354 0 / 0 / 0 / 6-Shogaol 31.298 1 O-Gln214 0 / 0 / 8-Shogaol 37.7374 1 O-Asn218 0 / 0 / 10-Shogaol 42.1221 0 / 0 / 0 / Ar-Curcumene 26.7476 0 / 0 / 0 / β-Bisabolene 24.9395 0 / 0 / 0 / β-Sesquiphelandrene 25.8704 0 / 0 / 0 / 6-Gingerdione 33.6531 0 / 0 / 0 / (−)-Zingiberene 23.3969 0 / 0 / 0 / Methyl-6-isogingerol 30.036 2 H-Gln214 O-Asn217 0 / 0 / CYP2D6 (PDB ID: 2F9Q) 6-Gingerol 49.7194 4 H-Arg441 O-His376 O-Arg101 O-Arg101 0 / 0 / 8-Gingerol 55.2159 4 H-Arg441 O-Arg101 O-Arg101 O-His376 0 / 0 / 10-Gingerol 57.6051 3 H-Arg441 O-Arg10 O-Arg101 0 / 0 / 6-Shogaol 46.6251 3 H-Arg441 O-Arg 101 O-His376 0 / 0 / 8-Shogaol 52.6567 3 H-Arg441 O-Arg101 O-His376 0 / 0 / 10-Shogaol 56.3996 3 O-His376 O-Arg101 O-Arg101 0 / 0 / Ar-Curcumene 29.9457 0 / 0 / 0 / β-Bisabolene 30.5663 0 / 0 / 0 / β-Sesquiphelandrene 28.6495 0 / 0 / 0 / 6-Gingerdione 50.0314 4 H-Arg441 O-Arg101 O-Arg101 O-His376 0 / 0 / (−)-Zingiberene 29.6369 0 / 0 / 0 / Methyl-6-isogingerol 51.8517 1 O-Arg101 0 / 0 / CYP3A4 (PDB ID: 1W0F) 6-Gingerol 51.1796 2 H-Ala305 H-Glu374 0 / 0 / 8-Gingerol 53.5899 2 H-Ala305 H-Glu374 0 / 0 / 10-Gingerol 54.8047 1 H-Glu374 0 / 0 / 6-Shogaol 49.1685 1 H-Ala305 0 / 0 / 8-Shogaol 53.9844 1 H-Ala305 0 / 0 / 10-Shogaol 63.0781 1 H-Ala305 0 / 0 / Ar-Curcumene 28.8825 0 / 0 / 0 / β-Bisabolene 27.4614 0 / 0 / 0 / β-Sesquiphelandrene 26.3732 0 / 0 / 0 / 6-Gingerdione 52.9237 2 H-Ala305 O-Arg105 0 / 0 / (−)-Zingiberene 27.9257 0 / 0 / 0 / Methyl-6-isogingerol 47.7586 0 / 0 / 0 / Abbreviation: CYP, cytochrome P450.

16 – 18 Briefly, the crystal structures of human CYP1A2 (protein data bank [PDB] code 2HI4), 2C9 CYP2C9 (PDB code 1OG2), 2C19 (PDB code 4GQS), 2D6 (PDB code 2F9Q), and 3A4 (PDB code 1W0F) were obtained from the Protein Data Bank ( http://www.rcsb.org/pdb/ ).

Publication Year: 2015