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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
1ikxPNUGag-Pol polyprotein2.7.7.49

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
1ikxPNUGag-Pol polyprotein2.7.7.491.000
3megT27Gag-Pol polyprotein2.7.7.490.619
1revTB9Gag-Pol polyprotein2.7.7.490.597
4i7fNVEGag-Pol polyprotein2.7.7.490.593
1ikyMSDGag-Pol polyprotein2.7.7.490.591
1tl1H18Gag-Pol polyprotein2.7.7.490.588
3i0rRT3Gag-Pol polyprotein2.7.7.490.587
2vg7NNIGag-Pol polyprotein2.7.7.490.585
1s1wUC1Gag-Pol polyprotein2.7.7.490.584
1tl3H20Gag-Pol polyprotein2.7.7.490.583
1tktH12Gag-Pol polyprotein2.7.7.490.582
1tkzH16Gag-Pol polyprotein2.7.7.490.581
2ze2T27Gag-Pol polyprotein2.7.7.490.579
2rf2MRXGag-Pol polyprotein2.7.7.490.575
3ffi3OBGag-Pol polyprotein2.7.7.490.575
3med65BGag-Pol polyprotein2.7.7.490.569
2hndNVPGag-Pol polyprotein2.7.7.490.568
1hnvTBOGag-Pol polyprotein2.7.7.490.567
1s9eADBGag-Pol polyprotein2.7.7.490.565
1vruAAPGag-Pol polyprotein2.7.7.490.565
1ikwEFZGag-Pol polyprotein2.7.7.490.559
1ikvEFZGag-Pol polyprotein2.7.7.490.558
1rt4UC1Gag-Pol polyprotein2.7.7.490.558
2hnzPC0Gag-Pol polyprotein2.7.7.490.558
2vg5NNCGag-Pol polyprotein2.7.7.490.558
1fk9EFZGag-Pol polyprotein2.7.7.490.556
3meeT27Gag-Pol polyprotein2.7.7.490.556
4ko0JLJGag-Pol polyprotein2.7.7.490.553
1hpzAAPGag-Pol polyprotein2.7.7.490.546
3m8qDJZGag-Pol polyprotein2.7.7.490.546
3is9AC7Gag-Pol polyprotein2.7.7.490.543
1hquHBYGag-Pol polyprotein2.7.7.490.542
1c1bGCAGag-Pol polyprotein2.7.7.490.540
4kko1REGag-Pol polyprotein2.7.7.490.540
1s6qTPBGag-Pol polyprotein2.7.7.490.535
4i2pG73Gag-Pol polyprotein2.7.7.490.535
1rt2TNKGag-Pol polyprotein2.7.7.490.534
2opqHBQGag-Pol polyprotein2.7.7.490.529
4g1qT27Gag-Pol polyprotein2.7.7.490.528
1rt5UC2Gag-Pol polyprotein2.7.7.490.525
1tvrTB9Gag-Pol polyprotein2.7.7.490.524
2ban357Gag-Pol polyprotein2.7.7.490.521
4ifvT27Gag-Pol polyprotein2.7.7.490.521
2zd1T27Gag-Pol polyprotein2.7.7.490.520
3qlhT27Gag-Pol polyprotein2.7.7.490.520
1eetBFUGag-Pol polyprotein2.7.7.490.518
3mec65BGag-Pol polyprotein2.7.7.490.517
4id5T27Gag-Pol polyprotein2.7.7.490.517
1tkxGWBGag-Pol polyprotein2.7.7.490.516
3nbpJGZGag-Pol polyprotein2.7.7.490.509
1hniAAAGag-Pol polyprotein2.7.7.490.502
1jlgUC1Gag-Pol polyprotein2.7.7.490.501
3i0sRT7Gag-Pol polyprotein2.7.7.490.501
1rt7UC4Gag-Pol polyprotein2.7.7.490.497
4i2q1BTGag-Pol polyprotein2.7.7.490.492
1ep4S11Gag-Pol polyprotein2.7.7.490.485
4ig3T27Gag-Pol polyprotein2.7.7.490.482
2chz093Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.481
1osvCHCBile acid receptor/0.480
1v7aFRCAdenosine deaminase3.5.4.40.480
3m8p65BGag-Pol polyprotein2.7.7.490.479
1jlqSBNGag-Pol polyprotein2.7.7.490.477
2oppHBQGag-Pol polyprotein2.7.7.490.477
3lamKRPGag-Pol polyprotein2.7.7.490.476
4kwi1TJReductase homolog/0.474
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.473
3hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.473
1klmSPPGag-Pol polyprotein2.7.7.490.472
2vf0F89Thymidylate synthase/0.472
4fad0TBPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.472
2acwUPGGlycosyltransferase/0.471
1dhiMTXDihydrofolate reductase1.5.1.30.470
3dmjGWEPol protein/0.468
4gh5NADShort-chain dehydrogenase/reductase SDR/0.467
1zidZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.466
3lanKBTGag-Pol polyprotein2.7.7.490.466
4jib1L6cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.466
5uviZMAAdenosine receptor A2a/0.466
1fm4DXCMajor pollen allergen Bet v 1-L/0.465
1n4hREANuclear receptor ROR-beta/0.465
1ndzFR5Adenosine deaminase3.5.4.40.465
1kb9SMACytochrome b/0.464
2yboSAHMethyltransferase/0.463
3juhANPCasein kinase II subunit alpha2.7.11.10.463
3s1dZIRCytokinin dehydrogenase 11.5.99.120.463
4b4oNDPEpimerase family protein SDR39U1/0.463
4lmuQUESerine/threonine-protein kinase pim-12.7.11.10.463
1ezvSMACytochrome b/0.462
1fkoEFZGag-Pol polyprotein2.7.7.490.462
3r7cFADFAD-linked sulfhydryl oxidase ALR1.8.3.20.462
4grb0XGCasein kinase II subunit alpha2.7.11.10.462
4qe6JN3Bile acid receptor/0.462
2chx090Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.461
2po7CHDFerrochelatase, mitochondrial4.99.1.10.461
4dtiNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.461
1qxlFR8Adenosine deaminase3.5.4.40.460
4bqpNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.460
2fk8SAMHydroxymycolate synthase MmaA42.1.10.458
3icsADPCoenzyme A disulfide reductase/0.458
3own3OWRenin3.4.23.150.458
3sp9IL2Peroxisome proliferator-activated receptor delta/0.458
4ryvZEAProtein LlR18A/0.458
3cxhSMACytochrome b/0.457
4h50NAPBiphenyl dioxygenase ferredoxin reductase subunit/0.457
1x8lOXRRetinol dehydratase/0.456
4ucnMYAGlycylpeptide N-tetradecanoyltransferase/0.456
1ml6GBXGlutathione S-transferase A22.5.1.180.455
2bxmIMNSerum albumin/0.455
3apfBMWPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.455
3bfa9ODOdorant binding protein ASP1/0.455
2ibzSMACytochrome b/0.454
3m0eATPTranscriptional regulator (NtrC family)/0.454
3q5kD1UHeat shock protein 83-1/0.454
3tqhNDPQuinone oxidoreductase/0.454
4jvf17XRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.454
2j9lATPH(+)/Cl(-) exchange transporter 5/0.453
2prh238Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.453
3nj0PYVAbscisic acid receptor PYL2/0.453
4aoxFADSteroid monooxygenase/0.453
4fjz4FJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.453
4g1z0VPVitamin D3 receptor A/0.453
1fp2HMOIsoflavone-7-O-methyltransferase 82.1.1.1500.452
2jn3JN3Fatty acid-binding protein, liver/0.452
3vtcTK3Vitamin D3 receptor/0.452
2aibERGBeta-elicitin cinnamomin/0.451
3bfb9ODPheromone-binding protein ASP1/0.451
4geb0LDKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.451
1e90MYCPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.450
1l2jETCEstrogen receptor beta/0.450
1nqaNADGlyceraldehyde-3-phosphate dehydrogenase/0.450
2c7xNRBCytochrome P450 monooxygenase PikC/0.450
2pr2DG1Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.450
3bejMUFBile acid receptor/0.450
3gc9B45Mitogen-activated protein kinase 112.7.11.240.450
3s79ASDAromatase1.14.14.140.450
3vtdTKDVitamin D3 receptor/0.450
4hxyNDPPlm1/0.450
4wdb2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.450
1f123HCHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.449
1jlaTNKGag-Pol polyprotein2.7.7.490.449
1xddAAYIntegrin alpha-L/0.449
2h96893Mitogen-activated protein kinase 82.7.11.240.449
3zoiM2WIsopenicillin N synthase1.21.3.10.449
4c2zMYAGlycylpeptide N-tetradecanoyltransferase 1/0.449
1ot7IU5Bile acid receptor/0.448
2nu9COASuccinate--CoA ligase [ADP-forming] subunit alpha6.2.1.50.448
3k2xI5A2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase/0.448
4c2yMYAGlycylpeptide N-tetradecanoyltransferase 1/0.448
4iaq2GM5-hydroxytryptamine receptor 1B/0.448
5a3bAPRSIR2 family protein/0.448
5k2bZMAAdenosine receptor A2a/0.448
1mb9ATPCarboxyethyl-arginine beta-lactam-synthase6.3.3.40.447
1yqj6NPMitogen-activated protein kinase 14/0.447
2aq8NAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.447
2ay95PVAromatic-amino-acid aminotransferase2.6.1.570.447
2om9AJAPeroxisome proliferator-activated receptor gamma/0.447
3a9wNADNDP-sugar epimerase/0.447
3d7kD7KBenzaldehyde lyase/0.447
3ielU5PRibonuclease TTHA02523.10.447
3qlrNDPDihydrofolate reductase1.5.1.30.447
4dbzNDPPutative ketoacyl reductase1.3.10.447
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.447
2nmtNHMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.446
3h18PMSEsterase/lipase/0.446
3zcw4A2Kinesin-like protein KIF11/0.446
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.446
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.445
1f28UMPThymidylate synthase2.1.1.450.445
1lb9DNQGlutamate receptor 2/0.445
1s1tUC1Gag-Pol polyprotein2.7.7.490.445
2aqkNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.445
2hcdBIVVitamin D3 receptor A/0.445
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.445
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.445
2lbaCHOFatty acid binding protein 6/0.445
2nv6ZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.445
2v4lABJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.445
2z7gEH9Adenosine deaminase3.5.4.40.445
3qm4PN0Cytochrome P450 2D6/0.445
4imoPWZProstaglandin-H2 D-isomerase5.3.99.20.445
4nky3QZSteroid 17-alpha-hydroxylase/17,20 lyase/0.445
5k2cZMAAdenosine receptor A2a/0.445
1f17NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.444
1fpqSAMIsoliquiritigenin 2'-O-methyltransferase/0.444
2hc4VDXVitamin D3 receptor A/0.444
2qd4CHDFerrochelatase, mitochondrial4.99.1.10.444
3c3eFO12-phospho-L-lactate transferase/0.444
3iro2CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.444
3nr4PYVAbscisic acid receptor PYL2/0.444
3ozd4CTS-methyl-5'-thioadenosine phosphorylase/0.444
3r374CO4-hydroxybenzoyl-CoA thioesterase3.1.2.230.444
3vspEK8Peroxisome proliferator-activated receptor gamma/0.444
4iarERM5-hydroxytryptamine receptor 1B/0.444
4z9g1Q5Corticotropin-releasing factor receptor 1/0.444
1blzACVIsopenicillin N synthase1.21.3.10.443
1cx2S58Prostaglandin G/H synthase 21.14.99.10.443
1fduESTEstradiol 17-beta-dehydrogenase 11.1.1.620.443
2i0zFADNAD(FAD)-utilizing dehydrogenases/0.443
2iodMYCDihydroflavonol 4-reductase1.1.1.2190.443
3w5rLOAVitamin D3 receptor/0.443
4bbhNHWGlycylpeptide N-tetradecanoyltransferase/0.443
4cf7ADPAdenylate kinase/0.443
4e37NDPCatalase1.11.1.60.443
4em9TCEPeroxisome proliferator-activated receptor gamma/0.443
4lhtCNL1,8-cineole 2-endo-monooxygenase1.14.13.1560.443
4ocvANPAminoglycoside phosphotransferase/0.443
4okx198Androgen receptor/0.443
4pkl1GHUncharacterized protein/0.443
5cpbNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.443
1bvrTHTEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
1dkfBMSRetinoic acid receptor alpha/0.442
1kt3RTLRetinol-binding protein 4/0.442
1ndeMONEstrogen receptor beta/0.442
1sj0E4DEstrogen receptor/0.442
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.442
3lfcZ86Mitogen-activated protein kinase 14/0.442
3pe6ZYHMonoglyceride lipase/0.442
4a31MYAGlycylpeptide N-tetradecanoyltransferase/0.442
4dc0NDPPutative ketoacyl reductase1.3.10.442
4rpgFADUDP-galactopyranose mutase5.4.99.90.442
5hs1VORLanosterol 14-alpha demethylase/0.442
4uhrNGIAdenosine receptor A2a/0.442
1cc2FADCholesterol oxidase1.1.3.60.441
1chwHXCChalcone synthase 22.3.1.740.441
1hfqMOTDihydrofolate reductase1.5.1.30.441
1jlcFTCGag-Pol polyprotein2.7.7.490.441
1kqwRTLCellular retinol-binding protein type II/0.441
1py5PY1TGF-beta receptor type-12.7.11.300.441
1rtiHEFGag-Pol polyprotein2.7.7.490.441
1t88CAMCamphor 5-monooxygenase1.14.15.10.441
2jdsL20cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
2qd5CHDFerrochelatase, mitochondrial4.99.1.10.441
2z6dFMNPhototropin-22.7.11.10.441
3gcoVAL_TYR_GLN_PHESerine endoprotease DegS3.4.21.1070.441
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.441
3ml8ML8Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.441
3r3f4CO4-hydroxybenzoyl-CoA thioesterase3.1.2.230.441
3zw3ZW3Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.441
4a87NARMajor pollen allergen Bet v 1-A/0.441
4cd2FOLDihydrofolate reductase1.5.1.30.441
1bk0ACVIsopenicillin N synthase1.21.3.10.440
1v79FR7Adenosine deaminase3.5.4.40.440
2aqhNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440
2gjnFMNNitronate monooxygenase1.13.12.160.440
2j14GNIPeroxisome proliferator-activated receptor delta/0.440
2zjwREFCasein kinase II subunit alpha2.7.11.10.440
3clbNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.440
3gobHXXDdmC/0.440
3lj3WYEPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
3w0yDS4Vitamin D3 receptor/0.440
3wmxNADNAD dependent epimerase/dehydratase/0.440
3zkyWT4Isopenicillin N synthase1.21.3.10.440
4k2xFADPolyketide oxygenase/hydroxylase/0.440
4mq12C3Dual specificity tyrosine-phosphorylation-regulated kinase 1A2.7.12.10.440
4pd6URINucleoside permease/0.440
4q71FADBifunctional protein PutA/0.440