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PDB ID Mentions in PubMed Central Article count: 7

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PDB ID Mentions in PubMed Central

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Development and validation of an improved algorithm for overlaying flexible molecules.

(2012) J Comput Aided Mol Des 26

PubMed: 22538643 | PubMedCentral: PMC3348445 | DOI: 10.1007/s10822-012-9573-y

Table 1 Test sets Protein Number of complexes PDB codes Protein kinase 5 (PK5) 2 1v0o, 1v0p Fatty acid binding protein (FABP) 3 1tou, 1tow, 2hnx Neprilysin (NEP) 4 1dmt, 1r1h, 1r1j, 1y8j Dihyd... ofolate reductase (DHFR) 6 1drf, 1hfr, 1mvt, 1pd9, 1s3v, 2dhf Checkpoint kinase (Chk1) 16 1nvq, 1nvr, 1nvs, 1zlt, 1zys, 2br1, 2brb, 2brg, 2brh, 2brm, 2bro, 2c3l, 2cgu, 2cgw, 2cgx, 2hog Neuraminidase (NEU) 11 1a4g, 1a4q, 1b9s, 1b9t, 1b9v, 1inf, 1inv, 1ivb, 1nsc, 1nsd, 1vcj Carbonic anhydrase (CA) 13 1bn3, 1bn4, 1bnq, 1cim, 1eou, 1if7, 1oq5, 1xpz, 1zgf, 1zh9, 2eu3, 2hoc, 2nng Adenosine deaminase (ADA) 11 1krm, 1ndv, 1ndw, 1ndy, 1o5r, 1qxl, 1uml, 1v7a, 1v79, 1wxy, 2e1w Heat shock protein 90 (HSP) 10 1byq, 1uy8, 1yc1, 1yc4, 1yet, 2bsm, 2byi, 2bz5, 2cct, 2uwd Acetylcholinesterase (AChE) 11 1dx6, 1e66, 1eve, 1gpk, 1gpn, 1h23, 1w4l, 1zgb, 2ack, 2c5g, 2ckm Table 2 Test subsets Protein/subset Number of complexes PDB codes ADA/1 10 1ndv, 1ndw, 1ndy, 1o5r, 1qxl, 1uml, 1v7a, 1v79, 1wxy, 2e1w ADA/2 4 1o5r, 1qxl, 1uml, 1wxy ADA/3 4 1ndv, 1o5r, 1qxl, 1uml HSP/1 7 1yc1, 1yc4, 2bsm, 2byi, 2bz5, 2cct, 2uwd HSP/2 3 1byq, 1uy8, 2cct AChE/1 9 1dx6, 1e66, 1gpk, 1gpn, 1h23, 1w4l, 1zgb, 2ack, 2ckm AChE/2 4 1h23, 1w4l, 1zgb, 2ckm Ligand models were created with CORINA [ 38 ] with addition of required hydrogen atoms.

The hydrophobic side chains of the 1bn3, 1bn4, 1bnq, 1if7, 1oq5, 1xpz, 1zh9 and 2hoc ligands are overlaid about as well as in the true overlay (which is to say, not very), but in the wrong position (that is, the ligand conformations are different from those in the true overlay).

Publication Year: 2012


Variability in docking success rates due to dataset preparation.

(2012) J Comput Aided Mol Des 26

PubMed: 22566074 | PubMedCentral: PMC3397132 | DOI: 10.1007/s10822-012-9570-1

Table 2 Complexes requiring capping of chain termini or chain breaks Complexes requiring capping of chain termini  1GKC 1MEH 1Q41 1V48  1GM8 1 MMV 1R55 1V4S  1G... K 1 MZC 1R9O 1W1P  1HNN 1N1M 1S19 1W2G  1HP0 1N2J 1SJ0 1XM6  1HWI 1N2V 1SQN 1XOQ  1HWW 1N46 1T46 1XOZ  1IG3 1OF1 1T9B 1Y6B  1J3J 1OF6 1TT1 1YGC  1JD0 1OPK 1TZ8 1YQY  1JJE 1OQ5 1U1C 1YV3  1JLA 1OYT 1U4D 1YVF  1K3U 1P2Y 1UML 1YWR  1LPZ 1P62 1UNL 2BM2  1LRH 1PMN 1UOU 2BR1  1M2Z 1Q1G 1V0P 2BSM Complexes requiring capping of chain breaks  1GPK 1N46 1SJ0 1V48  1HP0 1NAV 1SQ5 1W2G  1HWI 1OF1 1SQN 1XM6  1J3J 1OF6 1T46 1XOQ  1JLA 1OYT 1T9B 1Y6B  1KE5 1P62 1U1C 1YV3  1L2S 1PMN 1U4D 1YWR  1MEH 1Q41 1UOU 1Z95  1MMV 1R9O 1V0P 2BR1 The ‘corrected’ ACS-Astex dataset After the session transpired at the ACS meeting, 3 structures from the ACS-Astex set (1GPK, 1HVY and 1S3V) were identified as containing an inverted stereocenter in the original dataset given to the participants compared to the original PDB structure.

Table 1 Complexes requiring additional preparation Inconsistent stereo configuration  1GKC 1L7F 1R55 1VCJ  1GM8 1M2Z 1R58 1W1P  1GPK 1MMV 1R9O 1W2G  1HP0 1OF1 1S19 1X8X  1HVY 1OF6 1S3V 1XM6  1HWI 1OYT 1SQ5 1YGC  1HWW 1P2Y 1SQN 1YQY  1K3U 1P62 1TT1 1YV3  1KE5 1Q1G 1UML 1YWR  1KZK 1R1H 1V0P Co-factors with incorrect number of hydrogens  1G9V 1KZK 1Q1G 1W1P  1HWI 1M2Z 1Q4G 1W2G  1IA1 1MMV 1R9O 1XM6  1J3J 1OPK 1T9B 1XOQ  1JJE 1P62 1TZ8 Alternate locations missing hydrogens  1GM8 1OPK 1T9B 1XOZ  1HNN 1OQ5 1TZ8 1Y6B  1HP0 1Q4G 1UOU 1YV3  1IA1 1R1H 1VCJ 1YWR  1KZK 1S19 1W1P 1Z95  1L2S 1S3V 1X8X 2BR1  1N46 1T46 1XOQ The ‘modified’ ACS-Astex dataset Upon closer examination of some of the complexes it was noted that the hydrogen bond network was not optimal and therefore further optimization was warranted.

Table 6 Docking failures on corrected ACS-Astex set PDB code Failure type Minimum RMSD (Å) Present in binding site Top 1 Top 30 Water Metal 1g9v Placement 2.51 2.24 X 1gm8 Placement 3.20 2.69 X 1hp0 Scoring 2.93 1.07 X 1hvy Scoring 2.13 1.39 X 1jd0 Scoring 4.96 1.68 X 1l2s Scoring 3.65 0.80 1mzc Placement 3.66 2.92 X 1n2v Scoring 2.23 1.14 1oq5 Scoring 3.47 1.00 X 1owe Scoring 3.18 1.09 X 1q1 g Scoring 2.28 1.91 X 1r58 Placement 2.86 2.84 1sq5 Placement 4.96 2.55 X 1xm6 Scoring 2.40 0.50 X X 1y6b Placement 4.72 2.97 1ygc Placement 3.04 3.04 X Nearly half of the failure cases (8) were due to placement failure, where the docker was unable to generate any pose under 2 Å RMSD.

Publication Year: 2012


Automating crystallographic structure solution and refinement of protein-ligand complexes.

(2014) Acta Crystallogr D Biol Crystallogr 70

PubMed: 24419387 | PubMedCentral: PMC3919266 | DOI: 10.1107/S139900471302748X

( a ) PDB entry 1oq5 .

PDB code Re-refined R work / R free Pipeline R work / R free Placed/present Ligand r.m.s.d.(s) (Å) 1b9v 0.175/0.202 0.200/0.224 1/1 0.65 1br6 0.180/0.224 0.192/0.225 1/1 0.20 1cx2 0.245/0.308 0.250/0.362 0/4 — 1exa 0.169/0.192 0.182/0.213 1/1 0.06 1fcx 0.135/0.167 0.152/0.181 1/1 0.13 1fcz 0.141/0.175 0.157/0.182 1/1 0.08 1fjs 0.158/0.204 0.231/0.255 0/1 — 0.178/0.208 1/1 C 0.59 1g9v 0.141/0.166 0.135/0.171 1/2 0.17 0.136/0.171 2/2 C 0.16, 0.17 1hp0 0.163/0.216 0.173/0.227 2/2 P 0.31, 2.04 1hq2 0.121/0.160 0.134/0.166 1/1 0.10 1hwi 0.165/0.189 0.177/0.198 4/4 0.32–0.44 1hww 0.136/0.167 0.222/0.248 0/1 — 1k3u 0.135/0.162 0.137/0.165 1/1 0.05 1l2s 0.147/0.168 0.168/0.195 2/3 0.15, 0.16 1ml1 0.159/0.208 0.173/0.208 6/6 0.25–0.86 1mq6 0.171/0.221 0.184/0.227 1/1 P 1.36 0.179/0.230 1/1 C 0.68 1mzc 0.146/0.168 0.152/0.168 1/1 P 2.51 1n2j 0.168/0.193 0.185/0.210 2/2 0.10, 0.25 1of1 0.156/0.179 0.175/0.197 2/2 0.11, 0.13 1of6 0.173/0.191 0.208/0.230 8/8 0.11–1.82 1oq5 0.120/0.164 0.231/0.264 0/1 — 0.148/0.188 1/1 C 0.86 1pmn 0.190/0.224 0.218/0.249 1/1 0.53 1q1g 0.156/0.185 0.195/0.214 6/6 0.18–0.63 1q41 0.182/0.195 0.207/0.222 2/2 0.19, 0.30 1qhi 0.214/0.253 0.348/0.403 0/1 — 1r9o 0.162/0.193 0.240/0.284 1/1 0.39 1tt1 0.147/0.171 0.158/0.182 2/2 0.17, 0.19 1u4d 0.187/0.206 0.200/0.219 2/2 P 0.64, 0.67 1unl 0.190/0.214 0.264/0.291 0/1 — 0.246/0.276 1/1 C 0.98 1w1p 0.196/0.230 0.225/0.257 2/2 0.22, 0.30 1w2g 0.177/0.198 0.204/0.221 2/2 0.26, 0.56 1yqy 0.201/0.246 0.351/0.411 0/1 — 1yv3 0.151/0.184 0.169/0.193 1/1 0.19 2ack 0.159/0.185 0.446/0.507 — — 0.165/0.193 1/1 C 0.42 2br1 0.162/0.195 0.170/0.212 1/1 0.33 4cox 0.205/0.30 0.256/0.361 0/4 —

In some examples (such as PDB entry 1oq5 in the Iridium test set), LigandFit places the ligand(s) correctly but the pipeline rejects these models owing to a poor CC to the difference map.

(v) The pipeline also failed on PDB entry 1oq5 owing to a poor CC for the ligand density, despite nearly perfect placement (Fig. 3 ▶ a ).

Publication Year: 2014


Pathway analysis for drug repositioning based on public database mining.

(2014) J Chem Inf Model 54

PubMed: 24460210 | PubMedCentral: PMC3956470 | DOI: 10.1021/ci4005354

The crystal structure of a target protein carbonic anhydrase II (CA2) bound with celecoxib (PDB ID: 1OQ5) was retrieved from MMDB.

Publication Year: 2014


Inhibition mechanism of the intracellular transporter Ca2+-pump from sarco-endoplasmic reticulum by the antitumor agent dimethyl-celecoxib.

(2014) PLoS One 9

PubMed: 25003576 | PubMedCentral: PMC4086972 | DOI: 10.1371/journal.pone.0102083

All non-protein components were deleted from the protein structure and the CLX file in pdb format was obtained from PDB ID code 1OQ5.

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4383629

The PDB accession codes that contains the complex with the shown ligands are as follows: (a)1t46, (b)1oq5, and (c) 1tt1.

(a) A two-dimensional molecule, (b) A two-dimensional molecule and its Connolly surface corresponding to the red circular probe, and (c) the beta-shape corresponding to the probe, (d) the van der Waals model of a protein (PDB id 1oq5), (e) the Connolly surface for water molecule (with 1.4Å radius), and (f) the corresponding beta-shape.

Fig. 1(d), (e), and (f) show the van der Waals model of a protein (PDB id 1oq5), its Connolly surface for water molecule with 1.4Å radius, and the corresponding beta-shape.

Publication Year: 2015


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4383988

If a structure contains ligands, they are enumerated in the Ligand Chemical Component section (Figure 3a ) of the Structure Summary page, PDB ID 1OQ5 ( 41 ).

(a) Ligand Chemical Component widget on the Structure Summary page for Celecoxib bound to carbonic anhydrase II from PDB ID 1OQ5 ( 41 ).

Two new custom rendering options on the Jmol /JSmol page demonstrated using PDB ID 1OQ5 (Celecoxib bound to Carbonic Anhydrase II) ( 41 ).

Publication Year: 2014