Citations in PubMed

Primary Citation PubMed: 9677190 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 8

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.

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Automated docking screens: a feasibility study.

(2009) J Med Chem 52

PubMed: 19719084 | PubMedCentral: PMC2745826 | DOI: 10.1021/jm9006966

One ligand failed to be converted to SMILES automatically ( 1CKP ), but the rest of the 37 targets completed normally yielding a redocked and scored ligand.

Publication Year: 2009


Optimal assignment methods for ligand-based virtual screening.

(2009) J Cheminform 1

PubMed: 20150995 | PubMedCentral: PMC2820492 | DOI: 10.1186/1758-2946-1-14

target number actives number decoys number clusters a PDB code b ace c 46 1796 19 p 1o86 ache d 100 3859 18 1eve cdk2 e 47 2070 32 1ckp cox2 f 212 12606 44 1cx2 egfr g 365 15560 40 1m17 fxa h 64 2092 ... 9 1f0r hivrt i 34 1494 17 1rt1 inha j 57 2707 23 1p44 p38 k 137 6779 20 1kv2 pde5 l 26 1698 22 1xp0 pdgfrb m 124 5603 22 1t46 src n 98 5679 21 2src vegfr2 o 48 2712 31 1fgi Overview of the used data sets containing the number of actives, decoys, different chemotype clusters, and the PDB code of the complexed crystal structure which contains the search query.

Publication Year: 2009


Application of 3D Zernike descriptors to shape-based ligand similarity searching.

(2009) J Cheminform 1

PubMed: 20150998 | PubMedCentral: PMC2820497 | DOI: 10.1186/1758-2946-1-19

Target PDB Actives Decoys Decoys per active angiotensin-converting enzyme (ace) 1o86 46 1796 39.04 acetylcholinesterase (ache) 1eve 100 3859 38.59 cyclin-dependent kinase 2(cdk2) 1ckp 47 2070 44.04 cy... looxygenase-2(cox2) 1cx2 212 12606 59.46 epidermal growth factor receptor(egfr) 1m17 365 15560 42.63 factor Xa(fxa) 1f0r 64 2092 32.69 HIV reverse transcriptase(hivrt) 1rt1 34 1494 43.94 enoyl ACP reductase(inha) 1p44 57 2707 47.49 P38 mitogen activated protein(p38) 1kv2 137 6779 49.48 phosphodiesterase(pde5) 1xp0 26 1698 65.31 platelet derived growth factor receptor kinase(pdgfrb) 1t46 124 5603 45.19 tyrosine kinase SRC(src) 2src 98 5679 57.95 vascular endothelial growth factor receptor(vegfr2) 1fgi 48 2712 56.5 The third dataset from the National Cancer Institute (NCI) consists of 42,687 compounds derived from an assay measuring protection from HIV-1 infection of human CEM cells [ 57 ].

Publication Year: 2009


Genomics, evolution, and crystal structure of a new family of bacterial spore kinases.

(2010) Proteins 78

PubMed: 20077512 | PubMedCentral: PMC2860764 | DOI: 10.1002/prot.22663

Structure analysis Coordinates for structures other than YtaA were collected from the PDB 29 as follows: homoserine kinase 2 (HSK2, PDB ID: 2PPQ), choline kinase (ChoK, PDB ID: 1CKP), aminoglycoside p... osphotransferase (APH, PDB ID: 1L8T), and protein kinase A (PKA, PDB ID: 1CDK).

Table III Superposition of YtaA with Representative Structures from a Search with the Dali Server 60 Structure Classification PDB ID: chain Dali Z -score RMSD (Å) Aligned positions %ID Homoserine kinase 2 CAK 2PPQ:A 23.5 3.2 287 16 Choline/ethanolamine kinase CAK 3DXQ:A 18.9 3.9 265 13 YihE CAK 1ZYL:A 18.4 4.1 273 14 Choline kinase α-2 (ChoK) CAK 1CKP:A 15.6 3.9 259 14 Methylthioribose kinase (MTRK) CAK 2PUN:A 15.1 4.0 260 12 Aminoglycoside phosphotransferase (APH) CAK 1L8T:A 13.1 5.1 219 12 RIO1 Rio 1ZTH:C 9.9 3.6 168 15 Protein kinase A (PKA) ePK 1CDK:A 7.7 3.4 162 14 Structures with IDs in italics were used in analysis and comparisons with YtaA.

Publication Year: 2010


A method to enhance the hit ratio by a combination of structure-based drug screening and ligand-based screening.

(2008) Adv Appl Bioinform Chem 1

PubMed: 21918604 | PubMedCentral: PMC3169939 | DOI: null

Appendix B The protein databank (PDB) identifier list of the basic protein set is: 1a28, 1a42, 1a4g, 1a4q, 1abe1, 1abe2, 1abf1, 1abf2, 1aco, 1ai5, 1aoe, 1apt, 1apu, 1aqw, 1atl, 1b58, 1b9v, 1bma, 1byb,... 1byg, 1c1e, 1c5c, 1c83, 1cbs, 1cbx, 1cdg, 1ckp, 1com, 1coy, 1cps, 1cvu, 1d0l, 1d3h, 1dd7, 1dg5, 1dhf, 1dog, 1dr1, 1ebg, 1eed, 1ejn, 1epb, 1epo, 1ets, 1f0r, 1f0s, 1f3d, 1fen, 1fkg, 1fki, 1fl3, 1glp, 1hdc, 1hfc, 1hos, 1hpv, 1hsb, 1hsl, 1htf1, 1htf2, 1hyt, 1ida, 1ivb, 1jap, 1lah, 1lcp, 1lic, 1lna, 1lst, 1mdr, 1mld, 1mmq, 1mrg, 1mts, 1mup, 1nco, 1ngp, 1nis, 1okl, 1pbd, 1phd, 1phg, 1poc, 1ppc, 1pph, 1pso, 1qbr, 1qbu, 1qpq, 1rds, 1rne, 1rnt, 1rob, 1snc, 1srj, 1tlp, 1tmn, 1tng, 1tnh, 1tni, 1tnl, 1tyl, 1xid, 1xie, 1yee, 2aad, 2ack, 2ada, 2cht, 2cmd, 2cpp, 2ctc, 2fox, 2gbp, 2ifb, 2pk4, 2qwk, 2tmn, 3cla, 3cpa, 3erd, 3ert, 3tpi, 4lbd, 4phv, 5abp1, 5abp2, 5cpp, 5er1, 6rnt, and 7tim.

Publication Year: 2008


Virtual screening of specific insulin-like growth factor 1 receptor (IGF1R) inhibitors from the National Cancer Institute (NCI) molecular database.

(2012) Int J Mol Sci 13

PubMed: 23242155 | PubMedCentral: PMC3546745 | DOI: 10.3390/ijms131217185

The receptors and PDB IDs were CDK2 (1ckp), EGFr (1m17), FGFr1 (1agw), P38_MAP (1kv2), PDGFrb (model), SRC (2src), and VEGFr2 (1vr2).

Publication Year: 2012


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4114474

The DUD proteins include acetycholinesterase AChE (PDB code: 1EVE), human androgen receptor AR (PDB code: 1XQ2), human cyclin-dependent kinase 2 CDK2 (PDB code: 1CKP), human epidermal growth factor re... eptor EGFR (PDB code: 1M17), human mitogen-activated protein kinase 14 known as p38 (PDB code: 1KV2), human proto-oncogene tyrosine-protein kinase Src (PDB code: 2SRC), and cationic trypsin (PDB code: 1BJU).

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4493148

PDB ID Resolution (Å) 1GZ8 1.30 1JVP 1.53 1H00 1.60 1OIT 1.60 1URW 1.60 1H01 1.79 1H08 1.80 1E1X 1.85 1H07 1.85 1H0V 1.90 1OIR 1.91 1E1V 1.95 1PXI 1.95 1JSV 1.96 1PXO 1.96 1AQ1 2.00 1GII 2.00 ... KE6 2.00 1KE7 2.00 1KE8 2.00 1KE9 2.00 1PYE 2.00 1R78 2.00 1CKP 2.05 1DM2 2.10 1H0W 2.10 1DI8 2.20 1FVT 2.20 1GIJ 2.20 1KE5 2.20 1W0X 2.20 1VYZ 2.21 1PXJ 2.30 1PXP 2.30 1OIQ 2.31 1V1K 2.31 1P2A 2.50 1PXL 2.50 1PXN 2.50 1PF8 2.51 1PXM 2.53 1G5S 2.61 1GIH 2.80 1PXK 2.80 The final score used to rank compounds was purposely designed to be the average score across these 44 structures of CDK2 so as to account for structural variability.

Publication Year: 2015