Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
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
3di6PDZGag-Pol polyprotein2.7.7.49

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3di6PDZGag-Pol polyprotein2.7.7.491.000
3ffi3OBGag-Pol polyprotein2.7.7.490.697
3i0rRT3Gag-Pol polyprotein2.7.7.490.636
4i7fNVEGag-Pol polyprotein2.7.7.490.635
3dyaPZLGag-Pol polyprotein2.7.7.490.604
1ep4S11Gag-Pol polyprotein2.7.7.490.594
1hpzAAPGag-Pol polyprotein2.7.7.490.588
1hquHBYGag-Pol polyprotein2.7.7.490.584
1hnvTBOGag-Pol polyprotein2.7.7.490.583
1s1vTNKGag-Pol polyprotein2.7.7.490.581
3lamKRPGag-Pol polyprotein2.7.7.490.581
1jlaTNKGag-Pol polyprotein2.7.7.490.575
1rtiHEFGag-Pol polyprotein2.7.7.490.575
3i0sRT7Gag-Pol polyprotein2.7.7.490.574
2ban357Gag-Pol polyprotein2.7.7.490.573
3irxUDRGag-Pol polyprotein2.7.7.490.573
1revTB9Gag-Pol polyprotein2.7.7.490.571
1rt2TNKGag-Pol polyprotein2.7.7.490.568
1tvrTB9Gag-Pol polyprotein2.7.7.490.568
3lakKR1Gag-Pol polyprotein2.7.7.490.568
3lanKBTGag-Pol polyprotein2.7.7.490.565
3dolGWIPol protein/0.562
3m8qDJZGag-Pol polyprotein2.7.7.490.561
1klmSPPGag-Pol polyprotein2.7.7.490.553
3tamM06Gag-Pol polyprotein2.7.7.490.551
1rt1MKCGag-Pol polyprotein2.7.7.490.550
3drrR8EGag-Pol polyprotein2.7.7.490.548
4rw4494Gag-Pol polyprotein2.7.7.490.546
3dokGWJPol protein/0.545
2ze2T27Gag-Pol polyprotein2.7.7.490.544
3t195MAGag-Pol polyprotein2.7.7.490.543
2rkiTT1Gag-Pol polyprotein2.7.7.490.538
3drpR8EGag-Pol polyprotein2.7.7.490.532
1tkzH16Gag-Pol polyprotein2.7.7.490.529
4i2pG73Gag-Pol polyprotein2.7.7.490.525
2ic3HBYGag-Pol polyprotein2.7.7.490.522
4h4o506Gag-Pol polyprotein2.7.7.490.517
4mfb29TGag-Pol polyprotein2.7.7.490.517
5cyqT27Gag-Pol polyprotein2.7.7.490.517
1s9eADBGag-Pol polyprotein2.7.7.490.514
3dmjGWEPol protein/0.511
4h4uNDPBiphenyl dioxygenase ferredoxin reductase subunit/0.507
1ikvEFZGag-Pol polyprotein2.7.7.490.504
1tl1H18Gag-Pol polyprotein2.7.7.490.504
2ynfWHUGag-Pol polyprotein2.7.7.490.504
2vg7NNIGag-Pol polyprotein2.7.7.490.503
4ko0JLJGag-Pol polyprotein2.7.7.490.500
3nr4PYVAbscisic acid receptor PYL2/0.494
1vruAAPGag-Pol polyprotein2.7.7.490.493
1eetBFUGag-Pol polyprotein2.7.7.490.492
4i2q1BTGag-Pol polyprotein2.7.7.490.490
4ig3T27Gag-Pol polyprotein2.7.7.490.489
5a27MYAGlycylpeptide N-tetradecanoyltransferase/0.487
4wa9AXITyrosine-protein kinase ABL12.7.10.20.486
1umlFR4Adenosine deaminase3.5.4.40.482
3sgx0FWDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.482
3e01PZ2Gag-Pol polyprotein2.7.7.490.481
3qm4PN0Cytochrome P450 2D6/0.481
2jleI15Reverse transcriptase/RNaseH/0.480
2nmtNHMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.480
3irm1CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.480
4kko1REGag-Pol polyprotein2.7.7.490.480
3a60STURibosomal protein S6 kinase beta-12.7.11.10.479
1rt5UC2Gag-Pol polyprotein2.7.7.490.476
1rx8NAPDihydrofolate reductase1.5.1.30.476
2gtk208Peroxisome proliferator-activated receptor gamma/0.475
3iaeD7KBenzaldehyde lyase/0.475
1fm4DXCMajor pollen allergen Bet v 1-L/0.473
1hniAAAGag-Pol polyprotein2.7.7.490.473
2vn0TDZCytochrome P450 2C8/0.473
1hvyD16Thymidylate synthase2.1.1.450.472
1ia1NDPDihydrofolate reductase1.5.1.30.472
1rx1NAPDihydrofolate reductase1.5.1.30.472
2vnaNAPProstaglandin reductase 21.3.1.480.472
4a95NHWGlycylpeptide N-tetradecanoyltransferase/0.472
1ia2TQ4Dihydrofolate reductase1.5.1.30.471
3hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.471
3qlrNDPDihydrofolate reductase1.5.1.30.470
2hndNVPGag-Pol polyprotein2.7.7.490.469
3megT27Gag-Pol polyprotein2.7.7.490.469
1e7aPFLSerum albumin/0.468
1lwlDSOCamphor 5-monooxygenase1.14.15.10.468
3qlsNDPDihydrofolate reductase1.5.1.30.468
3wmxNADNAD dependent epimerase/dehydratase/0.468
1kt3RTLRetinol-binding protein 4/0.467
1kt6RTLRetinol-binding protein 4/0.467
2xvv9DNSerum albumin/0.467
4dc0NDPPutative ketoacyl reductase1.3.10.466
1wxyFRKAdenosine deaminase3.5.4.40.465
2hqpNDPDihydrofolate reductase1.5.1.30.465
3vt9YI4Vitamin D3 receptor/0.465
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.464
5kjePFBAlcohol dehydrogenase E chain1.1.1.10.464
1ai9NDPDihydrofolate reductase1.5.1.30.463
2vuw5IDSerine/threonine-protein kinase haspin2.7.11.10.463
4jv618FRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.463
1ikwEFZGag-Pol polyprotein2.7.7.490.462
3d3eD3ECorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.462
3is9AC7Gag-Pol polyprotein2.7.7.490.462
3tqhNDPQuinone oxidoreductase/0.462
1qxlFR8Adenosine deaminase3.5.4.40.461
3invNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.461
3mec65BGag-Pol polyprotein2.7.7.490.461
3qlwN22Dihydrofolate reductase1.5.1.30.461
4h9614QDihydrofolate reductase1.5.1.30.461
1felFENRetinol-binding protein 4/0.460
1o5rFR9Adenosine deaminase3.5.4.40.460
3nxxNDPDihydrofolate reductase1.5.1.30.460
4mq22C4Dual specificity tyrosine-phosphorylation-regulated kinase 1A2.7.12.10.460
1disBDMDihydrofolate reductase1.5.1.30.459
1tkxGWBGag-Pol polyprotein2.7.7.490.459
4ig01FGGag-Pol polyprotein2.7.7.490.459
1c1bGCAGag-Pol polyprotein2.7.7.490.458
2bxmIMNSerum albumin/0.458
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.458
3glmCOOGlutaconyl-CoA decarboxylase alpha subunit/0.458
1kt7RTLRetinol-binding protein 4/0.457
3c0g3AMPeripheral plasma membrane protein CASK2.7.11.10.457
4ia7BIVVitamin D3 receptor A/0.457
1diuBDMDihydrofolate reductase1.5.1.30.456
1f28UMPThymidylate synthase2.1.1.450.456
2ykeYKEHeat shock protein HSP 90-alpha/0.456
3be9P04Casein kinase II subunit alpha2.7.11.10.456
3byzH11Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.456
3vtdTKDVitamin D3 receptor/0.456
4b12NHWGlycylpeptide N-tetradecanoyltransferase/0.456
5eccNAPDehydrofolate reductase type I/0.456
1qiqACCIsopenicillin N synthase1.21.3.10.455
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.455
2iw94SPCyclin-dependent kinase 22.7.11.220.455
2vg5NNCGag-Pol polyprotein2.7.7.490.455
3lpkZ76Beta-secretase 13.4.23.460.455
3s7a684Dihydrofolate reductase1.5.1.30.455
4mq12C3Dual specificity tyrosine-phosphorylation-regulated kinase 1A2.7.12.10.455
1ndyFR3Adenosine deaminase3.5.4.40.454
1uuoBRFDihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.454
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.454
2y60M8FIsopenicillin N synthase1.21.3.10.454
3ch6311Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.454
3hjaNADGlyceraldehyde-3-phosphate dehydrogenase/0.454
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.454
1dhfFOLDihydrofolate reductase1.5.1.30.453
1fvv107Cyclin-dependent kinase 22.7.11.220.453
3q71AR6Poly [ADP-ribose] polymerase 142.4.2.300.453
4nb6444Nuclear receptor ROR-gamma/0.453
1ia4TQ6Dihydrofolate reductase1.5.1.30.452
1rx4DDFDihydrofolate reductase1.5.1.30.452
2bx8AZQSerum albumin/0.452
3ddw055Glycogen phosphorylase, liver form2.4.1.10.452
3zu2NAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.452
1fduESTEstradiol 17-beta-dehydrogenase 11.1.1.620.451
1m78NDPDihydrofolate reductase1.5.1.30.451
2r0pK2CPutative FAD-monooxygenase/0.451
2uzdC85Cyclin-dependent kinase 22.7.11.220.451
2ykjYKJHeat shock protein HSP 90-alpha/0.451
3eluSAMMethyltransferase/0.451
3g49NAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.451
3gwfFADCyclohexanone monooxygenase/0.451
3oafOAGDihydrofolate reductase1.5.1.30.451
4fkv61KCyclin-dependent kinase 22.7.11.220.451
5cdsPFBAlcohol dehydrogenase E chain1.1.1.10.451
2xlsFADPutative flavin-containing monooxygenase/0.450
2y05NAPProstaglandin reductase 1/0.450
3d84NDPDihydrofolate reductase1.5.1.30.450
3fcoIIGCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.450
3vfqAR6Poly [ADP-ribose] polymerase 142.4.2.300.450
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.450
5a3bAPRSIR2 family protein/0.450
1d3hA26Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.449
1kt4RTLRetinol-binding protein 4/0.449
1x7hNDPPutative ketoacyl reductase1.3.10.449
2c475IDCasein kinase I isoform gamma-2/0.449
2opqHBQGag-Pol polyprotein2.7.7.490.449
2zjwREFCasein kinase II subunit alpha2.7.11.10.449
3qlhT27Gag-Pol polyprotein2.7.7.490.449
3ua506XCytochrome P450 2B61.14.130.449
4a33MYAGlycylpeptide N-tetradecanoyltransferase/0.449
4c2xNHWGlycylpeptide N-tetradecanoyltransferase 2/0.449
5cdtPFBAlcohol dehydrogenase E chain1.1.1.10.449
1jlqSBNGag-Pol polyprotein2.7.7.490.448
1oiuN76Cyclin-dependent kinase 22.7.11.220.448
1tw2ERTCarminomycin 4-O-methyltransferase DnrK2.1.1.2920.448
2hcdBIVVitamin D3 receptor A/0.448
2oppHBQGag-Pol polyprotein2.7.7.490.448
3bzuA21Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.448
3vrwYS5Vitamin D3 receptor/0.448
1i7iAZ2Peroxisome proliferator-activated receptor gamma/0.447
1ml6GBXGlutathione S-transferase A22.5.1.180.447
1ndzFR5Adenosine deaminase3.5.4.40.447
1p93DEXGlucocorticoid receptor/0.447
3gwfNAPCyclohexanone monooxygenase/0.447
4feu537Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.447
4hfmNAP2-alkenal reductase (NADP(+)-dependent)/0.447
4pkl1GHUncharacterized protein/0.447
4tvbNADHomospermidine synthase2.5.1.440.447
3emlZMAAdenosine receptor A2a/0.447
1aqbRTLRetinol-binding protein 4/0.446
1e5qNDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming]1.5.1.100.446
1zg32HIIsoflavone 4'-O-methyltransferase/0.446
2hk9NAPShikimate dehydrogenase (NADP(+))/0.446
2idkC2FGlycine N-methyltransferase2.1.1.200.446
2igyA2TPlasmepsin 2/0.446
3eej53RUncharacterized protein/0.446
3eldSFGMethyltransferase/0.446
3oriAGSSerine/threonine protein kinase/0.446
3ruvANPChaperonin/0.446
3zhbNAPPutative dehydrogenase/0.446
4a32MYAGlycylpeptide N-tetradecanoyltransferase/0.446
4elg52JDihydrofolate reductase/0.446
4gkh0J9Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.446
4xldBRLPeroxisome proliferator-activated receptor gamma/0.446
4z9g1Q5Corticotropin-releasing factor receptor 1/0.446
1sqvUHDCytochrome b/0.445
1upw444Oxysterols receptor LXR-beta/0.445
1uzwCDHIsopenicillin N synthase1.21.3.10.445
2fzwNADAlcohol dehydrogenase class-31.1.1.10.445
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.445
4h9506UDihydrofolate reductase1.5.1.30.445
4lwaQ13Nitric oxide synthase oxygenase1.14.13.1650.445
4m87NADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.445
2aqhNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.444
2bfrADP[Protein ADP-ribosylglutamate] hydrolase AF_15213.2.20.444
2z3uCRRCytochrome P450/0.444
2zbaZBATrichothecene 3-O-acetyltransferase/0.444
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.444
3p99LNPLanosterol 14-alpha-demethylase/0.444
3qftNAPNADPH--cytochrome P450 reductase/0.444
3zbrNAP2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.444
4bchT7ZCyclin-dependent kinase 92.7.11.220.444
4hnc0UTMandelate racemase/0.444
4iarERM5-hydroxytryptamine receptor 1B/0.444
4pnmNU1Tankyrase-22.4.2.300.444
4rlh0WEEnoyl-[acyl-carrier-protein] reductase [NADH]/0.444
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.444
4ug71EVNitric oxide synthase oxygenase1.14.13.1650.444
4wecNADShort chain dehydrogenase/0.444
1nzdUPGDNA beta-glucosyltransferase/0.443
1tduDURThymidylate synthase/0.443
1zdwFLVPrenyltransferase/0.443
3axwTIDCasein kinase II subunit alpha2.7.11.10.443
3cgfJNFMitogen-activated protein kinase 102.7.11.240.443
3jynNDPQuinone oxidoreductase/0.443
3w0hW12Vitamin D3 receptor/0.443
4jufTPPBenzoylformate decarboxylase4.1.1.70.443
4z34ON7Lysophosphatidic acid receptor 1/0.443
1jlgUC1Gag-Pol polyprotein2.7.7.490.442
1susSAHCaffeoyl-CoA O-methyltransferase2.1.1.1040.442
1xurPB5Collagenase 33.4.240.442
2jn3JN3Fatty acid-binding protein, liver/0.442
2uzbC75Cyclin-dependent kinase 22.7.11.220.442
3fnu006HAP protein/0.442
3p8zSAHGenome polyprotein2.1.1.560.442
3sz0FADSulfide-quinone reductase/0.442
3zeiAWHO-acetylserine sulfhydrylase/0.442
3zkyWT4Isopenicillin N synthase1.21.3.10.442
4heu15JcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.442
4ia2BIVVitamin D3 receptor A/0.442
4rupH97Vitamin D3 receptor A/0.442
1d3gBREDihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.441
1drhNAPDihydrofolate reductase1.5.1.30.441
1hb1OCVIsopenicillin N synthase1.21.3.10.441
1m7aMQUDihydrofolate reductase1.5.1.30.441
1osvCHCBile acid receptor/0.441
1ppjANYCytochrome b/0.441
2dw4FADLysine-specific histone demethylase 1A10.441
2q5p241Peroxisome proliferator-activated receptor gamma/0.441
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.441
3dhoB2MStreptogramin A acetyltransferase2.3.10.441
3gkjHC3Niemann-Pick C1 protein/0.441
3jzfJZKBiotin carboxylase6.3.4.140.441
4dbzNDPPutative ketoacyl reductase1.3.10.441
4g95OAGDihydrofolate reductase1.5.1.30.441
4grb0XGCasein kinase II subunit alpha2.7.11.10.441
4l0qNADAlcohol dehydrogenase class-3/0.441
1aq1STUCyclin-dependent kinase 22.7.11.220.440
1dr5NAPDihydrofolate reductase1.5.1.30.440
1iyzNDPProbable quinone oxidoreductase/0.440
1j3jNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.440
1ya3STRMineralocorticoid receptor/0.440
1zx1CB1Ribosyldihydronicotinamide dehydrogenase [quinone]/0.440
2e9cB75Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.440
2gsdNADFormate dehydrogenase/0.440
2iw84SPCyclin-dependent kinase 22.7.11.220.440
2vagV25Dual specificity protein kinase CLK12.7.12.10.440
2vcmM11Isopenicillin N synthase1.21.3.10.440
3oq13OQCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.440
3sp6IL2Peroxisome proliferator-activated receptor alpha/0.440
4b5pACOAlpha-tubulin N-acetyltransferase 1/0.440
4fjz4FJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
4hjoAQ4Epidermal growth factor receptor2.7.10.10.440
4hle17VPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
4nmbFADBifunctional protein PutA/0.440
4oj4DIFPeroxisome proliferator-activated receptor gamma/0.440
4wdb2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.440