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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities are compared using Shaper.
For more information, please see the following publication: Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
1rtiHEFGag-Pol polyprotein2.7.7.49

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
1rtiHEFGag-Pol polyprotein2.7.7.491.000
3dolGWIPol protein/0.615
3dmjGWEPol protein/0.614
3dlgGWEGag-Pol polyprotein2.7.7.490.600
3i0rRT3Gag-Pol polyprotein2.7.7.490.581
3e01PZ2Gag-Pol polyprotein2.7.7.490.579
1rt1MKCGag-Pol polyprotein2.7.7.490.578
4h4o506Gag-Pol polyprotein2.7.7.490.575
3t195MAGag-Pol polyprotein2.7.7.490.573
4h4m494Gag-Pol polyprotein2.7.7.490.573
4mfb29TGag-Pol polyprotein2.7.7.490.555
2wonZZEGag-Pol polyprotein2.7.7.490.550
1jlaTNKGag-Pol polyprotein2.7.7.490.544
1s1vTNKGag-Pol polyprotein2.7.7.490.544
3di6PDZGag-Pol polyprotein2.7.7.490.544
2b5j3ACGag-Pol polyprotein2.7.7.490.541
3irxUDRGag-Pol polyprotein2.7.7.490.539
3c6uM22Gag-Pol polyprotein2.7.7.490.538
3dyaPZLGag-Pol polyprotein2.7.7.490.538
1c1c612Gag-Pol polyprotein2.7.7.490.527
1hpzAAPGag-Pol polyprotein2.7.7.490.527
3lakKR1Gag-Pol polyprotein2.7.7.490.527
3lamKRPGag-Pol polyprotein2.7.7.490.526
1hnvTBOGag-Pol polyprotein2.7.7.490.524
3dokGWJPol protein/0.523
3drrR8EGag-Pol polyprotein2.7.7.490.523
3drpR8EGag-Pol polyprotein2.7.7.490.520
3i0sRT7Gag-Pol polyprotein2.7.7.490.516
1tvrTB9Gag-Pol polyprotein2.7.7.490.512
3ffi3OBGag-Pol polyprotein2.7.7.490.510
2ban357Gag-Pol polyprotein2.7.7.490.507
3c6tM14Gag-Pol polyprotein2.7.7.490.507
2ic3HBYGag-Pol polyprotein2.7.7.490.505
4rw4494Gag-Pol polyprotein2.7.7.490.498
2rkiTT1Gag-Pol polyprotein2.7.7.490.495
3lanKBTGag-Pol polyprotein2.7.7.490.495
2ynhEURGag-Pol polyprotein2.7.7.490.493
3tamM06Gag-Pol polyprotein2.7.7.490.492
1hquHBYGag-Pol polyprotein2.7.7.490.487
1x8lOXRRetinol dehydratase/0.483
3lalKRVGag-Pol polyprotein2.7.7.490.483
2ynfWHUGag-Pol polyprotein2.7.7.490.479
1klmSPPGag-Pol polyprotein2.7.7.490.477
1ep4S11Gag-Pol polyprotein2.7.7.490.471
4l0qNADAlcohol dehydrogenase class-3/0.471
5d7pOCZNAD-dependent protein deacetylase sirtuin-23.5.10.469
3is9AC7Gag-Pol polyprotein2.7.7.490.468
1pq6965Oxysterols receptor LXR-beta/0.467
5cyqT27Gag-Pol polyprotein2.7.7.490.467
4a86H35Major pollen allergen Bet v 1-A/0.464
3nr4PYVAbscisic acid receptor PYL2/0.463
4i7fNVEGag-Pol polyprotein2.7.7.490.463
4fk3325Serine/threonine-protein kinase B-raf2.7.11.10.461
1fmlRTLRetinol dehydratase/0.460
4k9nTZDBenzoylformate decarboxylase4.1.1.70.460
4jib1L6cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.459
1yc2NADNAD-dependent protein deacylase 2/0.458
3a1l2CCCytochrome P450/0.457
3tk3CPZCytochrome P450 2B41.14.14.10.457
4a83DXCMajor pollen allergen Bet v 1-A/0.457
1fmjRTLRetinol dehydratase/0.456
2wd8VGFPteridine reductase/0.456
1x7hNDPPutative ketoacyl reductase1.3.10.455
4g310WHEukaryotic translation initiation factor 2-alpha kinase 32.7.11.10.455
3sn6P0GBeta-2 adrenergic receptor/0.455
4a81DXCMajor pollen allergen Bet v 1-A/0.454
5kf1ACOPredicted acetyltransferase/0.454
1ykdCMPAdenylate cyclase/0.453
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.453
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.452
3t8xT8XT-cell surface glycoprotein CD1b/0.452
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.452
1diuBDMDihydrofolate reductase1.5.1.30.451
2vcmM11Isopenicillin N synthase1.21.3.10.451
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.450
2b37NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.449
4b13NHWGlycylpeptide N-tetradecanoyltransferase/0.449
1errRALEstrogen receptor/0.448
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.448
4a87NARMajor pollen allergen Bet v 1-A/0.448
1obnASVIsopenicillin N synthase1.21.3.10.447
1tl7FOKAdenylate cyclase type 2/0.447
1tl7FOKAdenylate cyclase type 5/0.447
2ociTYCValacyclovir hydrolase3.10.447
3dl9V2HVitamin D 25-hydroxylase/0.447
3h0a9RARetinoic acid receptor RXR-alpha/0.447
3zkyWT4Isopenicillin N synthase1.21.3.10.447
4e0u0MVCyclic dipeptide N-prenyltransferase/0.447
2bxqIMNSerum albumin/0.446
2wueKEK4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase3.7.1.170.446
3ua506XCytochrome P450 2B61.14.130.445
4nc3ERM5-hydroxytryptamine receptor 2B/0.445
2ydoADNAdenosine receptor A2a/0.444
3d78NBBPheromone-binding protein ASP1/0.444
3bsyACOUDP-N-acetylbacillosamine N-acetyltransferase2.3.1.2030.443
4a33MYAGlycylpeptide N-tetradecanoyltransferase/0.443
4j6cSTRCytochrome P450 monooxygenase/0.443
4ruoBIVVitamin D3 receptor A/0.443
1w5aGTPCell division protein FtsZ 1/0.442
2xvv9DNSerum albumin/0.442
3gwfNAPCyclohexanone monooxygenase/0.442
3of2NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.442
4ejgNCTCytochrome P450 2A131.14.14.10.442
4iaq2GM5-hydroxytryptamine receptor 1B/0.442
4xbfFADLysine-specific histone demethylase 1A10.442
5d7q4I5NAD-dependent protein deacetylase sirtuin-23.5.10.442
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.441
4gi2NAPCrotonyl-CoA carboxylase/reductase/0.441
1xuoLA1Integrin alpha-L/0.440
2lbaCHOFatty acid binding protein 6/0.440
2yiuSMACytochrome b/0.440
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.440
3qlzQLZUncharacterized protein/0.440