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PDB ID Mentions in PubMed Central Article count: 1

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PDB ID Mentions in PubMed Central

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Binding of protein kinase inhibitors to synapsin I inferred from pair-wise binding site similarity measurements.

(2010) PLoS One 5

PubMed: 20808948 | PubMedCentral: PMC2922380 | DOI: 10.1371/journal.pone.0012214

Out of the 11 outliers, two entries (PDB entries 1aux and 1px2) drew our attention since they both describe the ATP-binding site of synapsin I. Despite a low homology (21%) between human Pim-1... (1yhs) and bovine synapsin I (1aux) amino acid sequences, the proposed 3-D alignment between both binding sites reveal remarkable shared features.

The full sc-PDB dataset was screened for similarity to the staurosporine-binding site of the Pim-1 kinase (PDB entry 1yhs) using standard settings of the SiteAlign v4.0 program.

Over 6,000 druggable protein-ligand binding sites from the sc-PDB database [39] were screened (step a, Fig. 1 ) for their similarity to the ATP-binding site of Pim-1 kinase (PDB entry 1yhs with bound inhibitor staurosporine) using the previously described SiteAlign algorithm [40] .

Active site detection was here achieved by specifying the chemical component HET code of the co-crystallized ligands (SAP for 1uax, STU for 1yhs).

B. 3-D SiteAlign alignment of human Pim-1 (1yhs, blue ribbons) bound to staurosporine (cyan sticks) and of bovine synapsin I (1aux, orange ribbons) bound to adenosine 5′-diphosphate monothiophosphate (yellow sticks).

PDB a d2 b Name HET c 2oxd 0.1008 Casein kinase II subunit alpha K32 2oxx 0.1038 Casein kinase II subunit alpha K22 1yi3 0.1056 Proto-oncogene serine/threonine-protein kinase Pim-1 LY2 1tqm 0.1083 RIO-type serine/threonine-protein kinase Rio2 ANP 3cy3 0.1176 Proto-oncogene serine/threonine-protein kinase Pim-1 JN5 3bgz 0.1199 Proto-oncogene serine/threonine-protein kinase Pim-1 VX3 3cy2 0.1233 Proto-oncogene serine/threonine-protein kinase Pim-1 MB9 2bik 0.1327 Proto-oncogene serine/threonine-protein kinase Pim-1 BI1 2c1a 0.1339 Protein kinase A I5S 1xr1 0.1350 Proto-oncogene serine/threonine-protein kinase Pim-1 ANP 1bl6 0.1368 Mitogen-activated protein kinase 14 SB6 1q8u 0.1385 cAMP-dependent protein kinase catalytic subunit alpha H52 3bi6 0.1388 Wee1-like protein kinase 396 3biz 0.1395 Wee1-like protein kinase 61E 2i0e 0.1400 Protein kinase C beta type PDS 1cm8 0.1405 Mitogen-activated protein kinase 12 ANP 2uzv 0.1423 cAMP-dependent protein kinase catalytic subunit alpha SS5 1yi4 0.1456 Proto-oncogene serine/threonine-protein kinase Pim-1 ADN 2hen 0.1467 Ephrin type-B receptor 2 ADP 2rkp 0.1474 Casein kinase II subunit alpha RFZ 2ojg 0.1481 Mitogen-activated protein kinase 1 19A 2z7s 0.1481 Ribosomal protein S6 kinase alpha-1 P01 2csn 0.1482 Casein kinase I homolog 1 CKI 1yhs 0.1483 Proto-oncogene serine/threonine-protein kinase Pim-1 STU 1mu 0.1508 Serine/threonine-protein kinase 6 ADN a PDB entry [10] .

C. 11 matching residues between the ATP-binding sites of Pim-1 (1yhs, cyan sticks) and synapsin I (yellow sticks).

Publication Year: 2010