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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
2ynfWHUGag-Pol polyprotein2.7.7.49

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2ynfWHUGag-Pol polyprotein2.7.7.491.000
4h4o506Gag-Pol polyprotein2.7.7.490.629
3drpR8EGag-Pol polyprotein2.7.7.490.618
3t195MAGag-Pol polyprotein2.7.7.490.609
3t1a5MAGag-Pol polyprotein2.7.7.490.607
3tamM06Gag-Pol polyprotein2.7.7.490.602
3c6uM22Gag-Pol polyprotein2.7.7.490.601
3c6tM14Gag-Pol polyprotein2.7.7.490.599
2be2R22Gag-Pol polyprotein2.7.7.490.589
3dyaPZLGag-Pol polyprotein2.7.7.490.586
3e01PZ2Gag-Pol polyprotein2.7.7.490.581
4mfb29TGag-Pol polyprotein2.7.7.490.578
3drrR8EGag-Pol polyprotein2.7.7.490.576
4rw6494Gag-Pol polyprotein2.7.7.490.575
3dmjGWEPol protein/0.572
4rw4494Gag-Pol polyprotein2.7.7.490.569
3lakKR1Gag-Pol polyprotein2.7.7.490.567
3dokGWJPol protein/0.564
3dlgGWEGag-Pol polyprotein2.7.7.490.559
2b5j3ACGag-Pol polyprotein2.7.7.490.556
2ynhEURGag-Pol polyprotein2.7.7.490.540
3ffi3OBGag-Pol polyprotein2.7.7.490.537
1jlaTNKGag-Pol polyprotein2.7.7.490.529
2wonZZEGag-Pol polyprotein2.7.7.490.529
3lalKRVGag-Pol polyprotein2.7.7.490.516
3dolGWIPol protein/0.513
1rt2TNKGag-Pol polyprotein2.7.7.490.505
2jleI15Reverse transcriptase/RNaseH/0.504
1c1bGCAGag-Pol polyprotein2.7.7.490.491
1rt1MKCGag-Pol polyprotein2.7.7.490.486
4i7fNVEGag-Pol polyprotein2.7.7.490.486
1rtiHEFGag-Pol polyprotein2.7.7.490.483
3lamKRPGag-Pol polyprotein2.7.7.490.483
3vt65YIVitamin D3 receptor/0.482
3dleGFAGag-Pol polyprotein2.7.7.490.480
3nbpJGZGag-Pol polyprotein2.7.7.490.479
4nb6444Nuclear receptor ROR-gamma/0.479
4q0a4OAVitamin D3 receptor A/0.479
2hc4VDXVitamin D3 receptor A/0.474
4erwSTUCyclin-dependent kinase 22.7.11.220.474
3dl9V2HVitamin D 25-hydroxylase/0.473
3fcoIIGCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.473
1ia4TQ6Dihydrofolate reductase1.5.1.30.471
3rk708ZCyclin-dependent kinase 22.7.11.220.471
1klmSPPGag-Pol polyprotein2.7.7.490.467
2o4rVD5Vitamin D3 receptor/0.467
3w0aDS5Vitamin D3 receptor/0.467
4ia3BIVVitamin D3 receptor A/0.467
3sw719KCyclin-dependent kinase 22.7.11.220.466
4fhh0U3Vitamin D3 receptor A/0.466
2nnhREACytochrome P450 2C8/0.464
1oirHDYCyclin-dependent kinase 22.7.11.220.463
2hamC33Vitamin D3 receptor/0.463
2hbhXE4Vitamin D3 receptor A/0.462
3di6PDZGag-Pol polyprotein2.7.7.490.462
3w5tLHPVitamin D3 receptor/0.462
1fmjRTLRetinol dehydratase/0.461
3m8qDJZGag-Pol polyprotein2.7.7.490.461
4oxyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.461
1aq1STUCyclin-dependent kinase 22.7.11.220.460
3vrwYS5Vitamin D3 receptor/0.460
4hfmNAP2-alkenal reductase (NADP(+)-dependent)/0.460
1c1c612Gag-Pol polyprotein2.7.7.490.459
4fhi0S4Vitamin D3 receptor A/0.459
2ardFDAFlavin-dependent tryptophan halogenase PrnA1.14.19.90.458
3rmf20ZCyclin-dependent kinase 22.7.11.220.458
3vt45YIVitamin D3 receptor/0.458
4bgePYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.458
4biiPYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.458
1rjkVDZVitamin D3 receptor/0.457
1rkgVD1Vitamin D3 receptor/0.457
3sqq99ZCyclin-dependent kinase 22.7.11.220.457
3w5p4OAVitamin D3 receptor/0.457
4g2h0VQVitamin D3 receptor A/0.457
4rupH97Vitamin D3 receptor A/0.457
1s1vTNKGag-Pol polyprotein2.7.7.490.456
3dr1C5DVitamin D3 receptor A/0.456
3w5rLOAVitamin D3 receptor/0.456
4gub0Y4Casein kinase II subunit alpha2.7.11.10.456
4ib4ERM5-hydroxytryptamine receptor 2B/0.456
1ndzFR5Adenosine deaminase3.5.4.40.455
4flh14KPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.455
4jib1L6cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.455
1cf3FADGlucose oxidase1.1.3.40.454
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.454
1ezvSMACytochrome b/0.454
2w06FRVCyclin-dependent kinase 22.7.11.220.454
3at4CCKCasein kinase II subunit alpha2.7.11.10.454
3jynNDPQuinone oxidoreductase/0.454
3kpkFADSulfide-quinone reductase/0.454
3tvuB37Acetyl-CoA carboxylase/0.454
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.453
1k6cMK1Gag-Pol polyprotein3.4.23.160.453
1rkhVD2Vitamin D3 receptor/0.453
2hb7O1CVitamin D3 receptor/0.453
2vzmNRBCytochrome P450 monooxygenase PikC/0.453
2wufKEM4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase3.7.1.170.453
1fm9570Peroxisome proliferator-activated receptor gamma/0.452
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.452
2hasC3OVitamin D3 receptor/0.452
3czr3CZCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.452
3kpzZNEVitamin D3 receptor/0.452
3vtdTKDVitamin D3 receptor/0.452
4acm7YGCyclin-dependent kinase 22.7.11.220.452
1rk3VDXVitamin D3 receptor/0.451
2w1hL0FCyclin-dependent kinase 22.7.11.220.451
3abaFLICytochrome P450/0.451
3p3zP3ZPutative cytochrome P450/0.451
1kt3RTLRetinol-binding protein 4/0.450
2c7xNRBCytochrome P450 monooxygenase PikC/0.450
3nwzCOABH2602 protein/0.450
3rk909ZCyclin-dependent kinase 22.7.11.220.450
4b7dQLECytochrome P450 monooxygenase PikC/0.450
4g210VPVitamin D3 receptor A/0.450
4k2xFADPolyketide oxygenase/hydroxylase/0.450
1kb9SMACytochrome b/0.449
1n4hREANuclear receptor ROR-beta/0.449
1w2xRCPAcetyl-CoA carboxylase/0.449
2ovhAS0Progesterone receptor/0.449
3i0rRT3Gag-Pol polyprotein2.7.7.490.449
3rm618ZCyclin-dependent kinase 22.7.11.220.449
3tmz06XCytochrome P450 2B41.14.14.10.449
4aw3MYVMycinamicin IV hydroxylase/epoxidase/0.449
1l2jETCEstrogen receptor beta/0.448
3a783EVVitamin D3 receptor/0.448
3sw418KCyclin-dependent kinase 22.7.11.220.448
3vt5YI2Vitamin D3 receptor/0.448
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.447
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.447
1yc2NADNAD-dependent protein deacylase 2/0.447
2hcdBIVVitamin D3 receptor A/0.447
2p1v5TNRetinoic acid receptor RXR-alpha/0.447
2wugHPK4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase3.7.1.170.447
2y98MIVMycinamicin IV hydroxylase/epoxidase/0.447
3tea4CO4-hydroxybenzoyl-CoA thioesterase3.1.2.230.447
4g1d0VKVitamin D3 receptor A/0.447
4h4m494Gag-Pol polyprotein2.7.7.490.447
5eaiFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.447
1menGARTrifunctional purine biosynthetic protein adenosine-32.1.2.20.446
4i2q1BTGag-Pol polyprotein2.7.7.490.446
4ia2BIVVitamin D3 receptor A/0.446
1e9hINRCyclin-dependent kinase 22.7.11.220.445
1gufNDPEnoyl-[acyl-carrier-protein] reductase 1, mitochondrial1.3.1.100.445
1pkfEPDEpothilone C/D epoxidase1.140.445
1v1k3FPCyclin-dependent kinase 22.7.11.220.445
2hb8MVDVitamin D3 receptor/0.445
4iarERM5-hydroxytryptamine receptor 1B/0.445
4ruoBIVVitamin D3 receptor A/0.445
1h1s4SPCyclin-dependent kinase 22.7.11.220.444
2hwrDRDPeroxisome proliferator-activated receptor gamma/0.444
2zlcVDXVitamin D3 receptor/0.444
3ez2ADPPlasmid partition protein A/0.444
3i0sRT7Gag-Pol polyprotein2.7.7.490.444
3zuxTCHTransporter/0.444
4eon1ROCyclin-dependent kinase 22.7.11.220.444
4iteTEYVitamin D3 receptor/0.444
4l455FIRibosomal protein S6 kinase beta-12.7.11.10.444
4o71CPBBromodomain-containing protein 4/0.444
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.443
2harOCCVitamin D3 receptor/0.443
3vt9YI4Vitamin D3 receptor/0.443
3w0c6DSVitamin D3 receptor/0.443
4nc3ERM5-hydroxytryptamine receptor 2B/0.443
4nka2K7Fibroblast growth factor receptor 1/0.443
1db1VDXVitamin D3 receptor/0.442
1p2a5BNCyclin-dependent kinase 22.7.11.220.442
2o3zAI7UDP-3-O-acyl-N-acetylglucosamine deacetylase/0.442
2y46MIVMycinamicin IV hydroxylase/epoxidase/0.442
3gcoVAL_TYR_GLN_PHESerine endoprotease DegS3.4.21.1070.442
3jqpA2PFerredoxin--NADP reductase, apicoplast/0.442
3r1sX73Cyclin-dependent kinase 22.7.11.220.442
4g1z0VPVitamin D3 receptor A/0.442
4hvi19STyrosine-protein kinase JAK32.7.10.20.442
4itfTFYVitamin D3 receptor/0.442
4j6cSTRCytochrome P450 monooxygenase/0.442
4z44FADFlavin-dependent tryptophan halogenase PrnA1.14.19.90.442
1n83CLRNuclear receptor ROR-alpha/0.441
1s19MC9Vitamin D3 receptor/0.441
2vn0TDZCytochrome P450 2C8/0.441
2zlaVDBVitamin D3 receptor/0.441
3m7rVDXVitamin D3 receptor/0.441
3w0yDS4Vitamin D3 receptor/0.441
1x8lOXRRetinol dehydratase/0.440
1y91CT9Cyclin-dependent kinase 22.7.11.220.440
2duv371Cyclin-dependent kinase 22.7.11.220.440
2vz6FEFCalcium/calmodulin-dependent protein kinase type II subunit alpha2.7.11.170.440
3ctj320Hepatocyte growth factor receptor2.7.10.10.440
3inwJZBHeat shock protein HSP 90-alpha/0.440
3iupNDPPossible NADH oxidoreductase/0.440
3lfnA27Cyclin-dependent kinase 22.7.11.220.440
3ml8ML8Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
3vt8YI3Vitamin D3 receptor/0.440
3zuyTCHTransporter/0.440
4a4wYFBPeroxisome proliferator-activated receptor gamma/0.440
4nky3QZSteroid 17-alpha-hydroxylase/17,20 lyase/0.440
4y8wSTRSteroid 21-hydroxylase/0.440