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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
3dolGWIPol protein

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3dolGWIPol protein/1.000
3e01PZ2Gag-Pol polyprotein2.7.7.490.629
4mfb29TGag-Pol polyprotein2.7.7.490.574
3dyaPZLGag-Pol polyprotein2.7.7.490.570
1rtiHEFGag-Pol polyprotein2.7.7.490.563
3c6tM14Gag-Pol polyprotein2.7.7.490.559
4h4o506Gag-Pol polyprotein2.7.7.490.554
3dmjGWEPol protein/0.552
3ffi3OBGag-Pol polyprotein2.7.7.490.543
1jlaTNKGag-Pol polyprotein2.7.7.490.541
1s1vTNKGag-Pol polyprotein2.7.7.490.533
3lakKR1Gag-Pol polyprotein2.7.7.490.531
4i7fNVEGag-Pol polyprotein2.7.7.490.531
3is9AC7Gag-Pol polyprotein2.7.7.490.530
3t195MAGag-Pol polyprotein2.7.7.490.528
4lsl1YQGag-Pol polyprotein2.7.7.490.526
3dlgGWEGag-Pol polyprotein2.7.7.490.522
3lamKRPGag-Pol polyprotein2.7.7.490.519
1rt2TNKGag-Pol polyprotein2.7.7.490.514
3i0rRT3Gag-Pol polyprotein2.7.7.490.513
1hpzAAPGag-Pol polyprotein2.7.7.490.511
4rw4494Gag-Pol polyprotein2.7.7.490.506
3drpR8EGag-Pol polyprotein2.7.7.490.502
3i0sRT7Gag-Pol polyprotein2.7.7.490.501
1klmSPPGag-Pol polyprotein2.7.7.490.498
2jleI15Reverse transcriptase/RNaseH/0.497
1c1c612Gag-Pol polyprotein2.7.7.490.496
3di6PDZGag-Pol polyprotein2.7.7.490.494
2ban357Gag-Pol polyprotein2.7.7.490.490
1hnvTBOGag-Pol polyprotein2.7.7.490.487
1rt1MKCGag-Pol polyprotein2.7.7.490.487
2ze2T27Gag-Pol polyprotein2.7.7.490.487
1ep4S11Gag-Pol polyprotein2.7.7.490.484
3lanKBTGag-Pol polyprotein2.7.7.490.484
1tvrTB9Gag-Pol polyprotein2.7.7.490.479
2rkiTT1Gag-Pol polyprotein2.7.7.490.479
2ynhEURGag-Pol polyprotein2.7.7.490.475
1fm4DXCMajor pollen allergen Bet v 1-L/0.474
1hquHBYGag-Pol polyprotein2.7.7.490.473
1tktH12Gag-Pol polyprotein2.7.7.490.473
3nbpJGZGag-Pol polyprotein2.7.7.490.469
1c1bGCAGag-Pol polyprotein2.7.7.490.468
1tkzH16Gag-Pol polyprotein2.7.7.490.466
3tamM06Gag-Pol polyprotein2.7.7.490.466
4l0qNADAlcohol dehydrogenase class-3/0.466
1fmjRTLRetinol dehydratase/0.463
3nr4PYVAbscisic acid receptor PYL2/0.462
2jn3JN3Fatty acid-binding protein, liver/0.461
1fmlRTLRetinol dehydratase/0.459
2ynfWHUGag-Pol polyprotein2.7.7.490.459
3lalKRVGag-Pol polyprotein2.7.7.490.456
4biiPYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.455
3t2yFADSulfide-quinone reductase/0.454
4i2q1BTGag-Pol polyprotein2.7.7.490.454
4wa9AXITyrosine-protein kinase ABL12.7.10.20.453
3t14FADSulfide-quinone reductase/0.452
2xvv9DNSerum albumin/0.451
3m8qDJZGag-Pol polyprotein2.7.7.490.451
1og5SWFCytochrome P450 2C9/0.450
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.449
3gwfNAPCyclohexanone monooxygenase/0.449
3sz0FADSulfide-quinone reductase/0.449
4j6bPLOCytochrome P450 monooxygenase/0.449
3vt5YI2Vitamin D3 receptor/0.448
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.447
2ic3HBYGag-Pol polyprotein2.7.7.490.447
3ey9TDPPyruvate dehydrogenase [ubiquinone]1.2.5.10.447
4dpdDHFBifunctional dihydrofolate reductase-thymidylate synthase/0.447
5cyqT27Gag-Pol polyprotein2.7.7.490.447
2zlaVDBVitamin D3 receptor/0.445
3drrR8EGag-Pol polyprotein2.7.7.490.445
4dl9NADS-(hydroxymethyl)glutathione dehydrogenase/0.445
1dr3HBIDihydrofolate reductase1.5.1.30.444
2nmtNHMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.444
5k2bZMAAdenosine receptor A2a/0.444
2acwUPGGlycosyltransferase/0.443
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.443
3qlrNDPDihydrofolate reductase1.5.1.30.443
3vrtYS2Vitamin D3 receptor/0.443
3zkpERBErythromycin C-12 hydroxylase1.14.13.1540.443
4j6cSTRCytochrome P450 monooxygenase/0.443
2z3uCRRCytochrome P450/0.442
2bheBRYCyclin-dependent kinase 22.7.11.220.440
3c0g3AMPeripheral plasma membrane protein CASK2.7.11.10.440
3sp9IL2Peroxisome proliferator-activated receptor delta/0.440
3ua506XCytochrome P450 2B61.14.130.440
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.440