Citations in PubMed

Primary Citation PubMed: 17391695 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 5

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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Atomic analysis of protein-protein interfaces with known inhibitors: the 2P2I database.

(2010) PLoS One 5

PubMed: 20231898 | PubMedCentral: PMC2834754 | DOI: 10.1371/journal.pone.0009598

Class # Family Complex a Number of Inhibitors b Source c Affinity d (nM) Ref I 1 BclX L /Bak 1bxl 8 PubMed 340 [27] I 2 MDM2/p53 1ycr 1ycq 3 PubMed 600 [28] I 3 XIAP BI... 3/CASPASE 9 1nw9 2 PubMed 20 [29] I 4 XIAP BIR3/SMAC 1g73 5 PubMed 420 [29] I 5 ZipA/FtsZ 1f47 4 PubMed 20,000 [30] II 6 Chagasin/Papain 3e1z 1 PDB 0.036 e [31] II 7 E2/E1 1tue 1 PubMed na [32] II 8 FKBP12/TGFR 1b6c 17 PDB na [33] II 9 IL-2/IL-2R 1z92 8 PubMed 10 [34] II 10 MMP1/TIMP1 2j0t 1 PDB 0.40 e [35] II 11 MMP3/TIMP1 1oo9 1 PDB 0.22 e [36] II 12 Subtilisin/Eglin C 1cse 1r0r 1to2 1 PDB 0.029 [37] – [39] II 13 Thrombin/Protein C inhibitor 3b9f 1 PDB na [40] II 14 Trypsin/Trypsin inhibitor 2uuy 3 PDB 0.02 [41] PPIs were subdivided into class I that correspond to protein/peptide interactions with less than six segments at the interface (families 1–5) and class II that represent more globular interacting domains with more segments (families 6–14).

Publication Year: 2010


Sampling the conformation of protein surface residues for flexible protein docking.

(2010) BMC Bioinformatics 11

PubMed: 21092317 | PubMedCentral: PMC3002368 | DOI: 10.1186/1471-2105-11-575

Table 1 The different docking test cases included in our experiments Complex PDB ID 1ACB 1AHW 1AK4 1AKJ 1AY7 1B6C 1BJ1 1BKD 1BUH 1BVK 1BVN 1CGI 1D6R 1DFJ 1DQJ 1E6E 1E6J 1EAW 1EER 1EWY 1FC2 1FSK 1GHQ 1... 9R 1IBR 1IQD 1KAC 1KTZ 1KXQ 1M10 1MAH 1ML0 1MLC 1NCA 1NSN 1QFW 1R0R 1S1Q 1SBB 1TMQ 1UDI 1VFB 1WEJ 1WQ1 1Y64 2AJF 2B42 2FD6 2I25 2JEL 2MTA 2QFW a 2SIC 2UUY 2VIS 7CEI a Note that the name 2QFW does not correspond to the actual PDB file with this ID.

Publication Year: 2010


Benchmarking and analysis of protein docking performance in Rosetta v3.2.

(2011) PLoS One 6

PubMed: 21829626 | PubMedCentral: PMC3149062 | DOI: 10.1371/journal.pone.0022477

PDB Difficulty | type N 5 µ(N 5 ) [σ(N 5 )] P success Irmsd CAPRI quality PDB Difficulty | type N 5 µ (N 5 ) [σ(N 5 )] P success Irmsd CAPRI quality 1OPH rigid-body | E... 5 5.0 [0.0] 1.00 0.23 *** 1YVB rigid-body | E 4 4.0 [0.9] 0.71 1.32 ** 1ML0 rigid-body | O 5 5.0 [0.0] 1.00 0.40 *** 1ZHI rigid-body | O 4 4.0 [0.9] 0.72 1.47 ** 1KTZ rigid-body | O 5 5.0 [0.0] 1.00 0.51 *** 1XQS medium | O 4 3.9 [1.0] 0.70 1.47 ** 1PPE rigid-body | E 5 5.0 [0.0] 1.00 0.91 *** 2OOB rigid-body | O 4 3.9 [1.2] 0.69 1.04 ** 1B6C rigid-body | O 5 5.0 [0.0] 1.00 1.51 ** 1DFJ rigid-body | E 4 3.6 [1.4] 0.57 1.39 ** 2HLE rigid-body | O 5 5.0 [0.2] 1.00 0.89 *** 1BJ1 rigid-body | AB 4 3.6 [1.2] 0.57 2.25 * 1KXP rigid-body | O 5 5.0 [0.2] 1.00 1.16 ** 2CFH medium | O 4 3.6 [1.1] 0.56 1.25 ** 2HRK medium | O 5 5.0 [0.2] 0.99 1.42 ** 1BVK rigid-body | A 3 3.5 [1.2] 0.51 1.77 ** 1QA9 rigid-body | O 5 5.0 [0.1] 1.00 0.59 *** 1AVX rigid-body | E 3 3.4 [1.1] 0.50 1.87 ** 1FSK rigid-body | AB 5 5.0 [0.1] 1.00 1.03 ** 1MAH rigid-body | E 3 3.4 [1.1] 0.50 1.94 ** 1JPS rigid-body | A 5 4.9 [0.5] 0.97 1.15 ** 1VFB rigid-body | A 4 3.4 [1.1] 0.50 1.96 ** 1AK4 rigid-body | O 5 4.9 [0.5] 0.97 1.36 ** 2SNI rigid-body | E 3 3.3 [1.1] 0.47 1.14 ** 1UDI rigid-body | E 5 4.9 [0.4] 0.98 2.17 * 1KXQ rigid-body | AB 3 3.3 [1.1] 0.44 1.25 ** 1D6R rigid-body | E 5 4.9 [0.3] 0.99 2.14 * 1BUH rigid-body | O 3 3.3 [1.1] 0.44 1.73 ** 7CEI rigid-body | E 5 4.8 [0.6] 0.94 0.79 *** 1XD3 rigid-body | O 3 3.3 [1.1] 0.45 2.69 * 2UUY rigid-body | E 5 4.7 [0.7] 0.93 1.30 ** 1E4K difficult | A 4 3.2 [1.3] 0.45 1.98 ** 1E6E rigid-body | E 5 4.7 [0.6] 0.94 0.79 *** 1E6J rigid-body | A 3 3.2 [1.2] 0.40 2.48 * 1SBB rigid-body | O 5 4.6 [0.7] 0.91 0.60 *** 1HIA rigid-body | E 3 3.2 [1.1] 0.40 1.95 ** 2C0L difficult | O 5 4.6 [0.7] 0.91 1.15 ** 2SIC rigid-body | E 3 3.1 [1.3] 0.40 0.59 *** 1IQD rigid-body | AB 5 4.5 [0.8] 0.89 1.26 ** 2FD6 rigid-body | A 3 3.1 [1.2] 0.38 1.85 ** 1AHW rigid-body | A 5 4.5 [0.7] 0.89 1.38 ** 1HE1 rigid-body | O 3 3.0 [1.2] 0.36 1.31 ** 1GCQ rigid-body | O 5 4.4 [0.8] 0.88 0.72 *** 2JEL rigid-body | AB 3 3.0 [1.1] 0.36 0.40 *** 1EAW rigid-body | E 4 4.4 [0.8] 0.87 1.31 ** 1AY7 rigid-body | E 3 2.9 [1.1] 0.32 1.55 ** 1FC2 rigid-body | O 4 4.4 [0.8] 0.84 1.53 ** 1WQ1 medium | O 3 2.8 [1.3] 0.30 1.48 ** 1GPW rigid-body | O 4 4.4 [0.8] 0.88 1.98 ** 2QFW rigid-body | AB 3 2.8 [1.2] 0.30 0.64 *** 2MTA rigid-body | E 4 4.3 [0.9] 0.81 0.66 *** 1IJK medium | E 3 2.8 [1.2] 0.28 2.35 * 1BVN rigid-body | E 4 4.0 [1.0] 0.72 1.35 ** 1NCA rigid-body | AB 3 2.7 [1.3] 0.27 0.46 *** 1CGI rigid-body | E 4 4.0 [1.0] 0.74 1.76 ** 2I25 rigid-body | A 3 2.2 [1.2] 0.15 1.80 ** 10.1371/journal.pone.0022477.

Publication Year: 2011


Evolution, expansion and expression of the Kunitz/BPTI gene family associated with long-term blood feeding in Ixodes Scapularis.

(2012) BMC Evol Biol 12

PubMed: 22244187 | PubMedCentral: PMC3273431 | DOI: 10.1186/1471-2148-12-4

Six protein modes (AAM93606, AAM93608, AAM93610 and AAM93612 from group II; AAM93632 and AAM93635 from group III) were aligned with other Kunitz/BPTI protein structures ( 1BF0 , 1BPI , 1BUN , 1DEM , 1... TK , 1DTX , 1SHP , 2CA7 , 2JOT , 2KCR , 2UUY , 2W8X ) using the MISTRAL online server.

Publication Year: 2012


Tryptogalinin is a tick Kunitz serine protease inhibitor with a unique intrinsic disorder.

(2013) PLoS One 8

PubMed: 23658744 | PubMedCentral: PMC3643938 | DOI: 10.1371/journal.pone.0062562

Tryptogalinin-Trypsin Docking Verifies an Induced Fit Recognition Mechanism Since the TdPI-trypsin crystallographic structure has been solved (PDB: 2UUY), we attempted to predict the tryptogalinin-try... sin complex by performing protein-protein docking.

Here, based on the TdPI-trypsin crystal (PDB: 2UUY), we added an 8Å cutoff between Lys13 and Asp191 for tryptogalinin.

Top two panels (A) show the coarse grain binding against the RMSD for two tryptogalinin models, Tryp1: the last snapshot of a 62 ns equilibration, and Tryp2, the snapshot with best superimposition to TdPI (its complex with trypsin) (PDB: 2UUY).

Intrinsic regional protein disorder (A) predicted by the GeneSilico MetaServer [37] for tryptogalinin, TdPI (PDB: 2UUY chain: B) and BPTI (PDB: 5PTI), respectively – ‘D’ represents the disordered region and dashes are ordered.

A comparison between (B) the best all-atom model for tryptogalinin (yellow) and the complex TdPI-trypsin crystal structure (PDB: 2UUY) (red) depict significant binding similarities.

The distance between Lys13 of tryptogalinin and the Asp191 of the trypsin binding site was always >8Å, whereas the distance between TdPI Lys39 and trypsin Asp191 is ∼3Å in the 2UUY crystallographic structure.

Publication Year: 2013