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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
3q6kSRO43.2 kDa salivary protein

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3q6kSRO43.2 kDa salivary protein/1.000
3zkyWT4Isopenicillin N synthase1.21.3.10.515
1h42FADFerredoxin--NADP reductase1.18.1.20.501
2w3aTOPDihydrofolate reductase1.5.1.30.498
4du6GTPGTP cyclohydrolase 1/0.493
3tfuPL8Adenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.492
2vqjTFGHistone deacetylase 43.5.1.980.485
1thz326Bifunctional purine biosynthesis protein PURH2.1.2.30.484
2y60M8FIsopenicillin N synthase1.21.3.10.484
4l4v1VYMajor histocompatibility complex class I-related gene protein/0.484
3zoiM2WIsopenicillin N synthase1.21.3.10.483
1bk0ACVIsopenicillin N synthase1.21.3.10.482
1obnASVIsopenicillin N synthase1.21.3.10.482
2jh6894Prothrombin3.4.21.50.482
1ogiFADFerredoxin--NADP reductase1.18.1.20.481
1hb3SCVIsopenicillin N synthase1.21.3.10.480
1qjfACSIsopenicillin N synthase1.21.3.10.479
4kxjP34Nucleoprotein/0.479
4z63ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.479
1hb1OCVIsopenicillin N synthase1.21.3.10.478
3q7jFBOTricorn protease-interacting factor F33.4.110.478
4bb3KKAIsopenicillin N synthase1.21.3.10.477
2zhf49UProthrombin3.4.21.50.476
2iviACWIsopenicillin N synthase1.21.3.10.475
2jb4A14Isopenicillin N synthase1.21.3.10.475
2vcmM11Isopenicillin N synthase1.21.3.10.475
4py06ATP2Y purinoceptor 12/0.475
1u1d181Uridine phosphorylase2.4.2.30.474
2vbdV10Isopenicillin N synthase1.21.3.10.474
1mj3HXCEnoyl-CoA hydratase, mitochondrial4.2.1.170.473
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.473
4hcy0YNTransketolase/0.473
5epoTUD7-alpha-hydroxysteroid deydrogenase/0.473
1eq2ADQADP-L-glycero-D-manno-heptose-6-epimerase/0.472
1queFADFerredoxin--NADP reductase1.18.1.20.472
1w06W05Isopenicillin N synthase1.21.3.10.472
2b82ADNClass B acid phosphatase3.1.3.20.472
2owb626Serine/threonine-protein kinase PLK12.7.11.210.472
4j521J3Serine/threonine-protein kinase PLK12.7.11.210.471
4jlj1NMDeoxycytidine kinase2.7.1.740.471
1b48HAGGlutathione S-transferase A42.5.1.180.470
1upw444Oxysterols receptor LXR-beta/0.470
1x8vESLLanosterol 14-alpha demethylase1.14.13.700.470
4jln18VDeoxycytidine kinase2.7.1.740.470
1umaIN2Prothrombin3.4.21.50.469
2qjpANJCytochrome b/0.469
3f3y4OABile salt sulfotransferase2.8.2.140.469
4e2yJHZMethyltransferase/0.469
4l7h1W1Beta-secretase 13.4.23.460.469
1aquESTEstrogen sulfotransferase, testis isoform2.8.2.40.468
4a4o664Serine/threonine-protein kinase PLK12.7.11.210.468
5bsrCOA4-coumarate--CoA ligase 26.2.1.120.468
1a4wQWEProthrombin3.4.21.50.467
1h36R88Squalene--hopene cyclase4.2.1.1290.467
1pr4MTPPurine nucleoside phosphorylase DeoD-type/0.467
1qiqACCIsopenicillin N synthase1.21.3.10.467
2cf8ESHProthrombin3.4.21.50.467
3nxrD2DDihydrofolate reductase1.5.1.30.467
5arkUMPRibonuclease 43.1.270.467
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.466
4kebFOLDihydrofolate reductase1.5.1.30.466
4ybnFADFlavin-nucleotide-binding protein/0.466
1w6jR71Lanosterol synthase5.4.99.70.465
2bn4FMNNADPH--cytochrome P450 reductase/0.465
4af6FADFerredoxin--NADP reductase, leaf isozyme, chloroplastic1.18.1.20.465
4ayy9MXProthrombin3.4.21.50.465
2bu9HFVIsopenicillin N synthase1.21.3.10.464
2zbwFADFerredoxin--NADP reductase/0.464
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.464
1blzACVIsopenicillin N synthase1.21.3.10.463
3tfyCOAN-alpha-acetyltransferase 502.3.10.463
4b66NAPL-ornithine N(5)-monooxygenase/0.463
4ubvCOASteroid 3-ketoacyl-CoA thiolase/0.463
1nqvLMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.462
1zgbA1EAcetylcholinesterase3.1.1.70.462
4b8wGDPGDP-L-fucose synthase1.1.1.2710.462
4bfuZVUPantothenate kinase2.7.1.330.462
1c4yIH3Prothrombin3.4.21.50.461
1oc1ASVIsopenicillin N synthase1.21.3.10.461
1uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.461
4jlm1NNDeoxycytidine kinase2.7.1.740.461
4rn615UProthrombin3.4.21.50.461
5irnADPNucleotide binding oligomerization domain containing 2/0.461
1ye6NAPNAD(P)H-dependent D-xylose reductase1.1.1.3070.460
4bfxZVXPantothenate kinase2.7.1.330.460
5c1mCLRMu-type opioid receptor/0.460
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.459
1u65CP0Acetylcholinesterase3.1.1.70.459
1xzqFONtRNA modification GTPase MnmE3.6.50.459
2ohiFMNType A flavoprotein FprA10.459
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.459
1cnfFADNitrate reductase [NADH]1.7.1.10.458
1d4pBPPProthrombin3.4.21.50.458
2x86ADPADP-L-glycero-D-manno-heptose-6-epimerase/0.458
2xk6EQHSerine/threonine-protein kinase Nek22.7.11.10.458
2y6fM9FIsopenicillin N synthase1.21.3.10.458
3dopNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.458
4afeGGYSerine/threonine-protein kinase Nek22.7.11.10.457
4bfzZVZPantothenate kinase2.7.1.330.457
4gt8ADPSensor protein VraS2.7.13.30.457
4j7hTRHPCZA361.3/0.457
4jsr1NQNAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.10.457
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.457
1ppjANYCytochrome b/0.456
2gdeSN3Prothrombin3.4.21.50.456
2jc6QPPCalcium/calmodulin-dependent protein kinase type 1D2.7.11.170.456
2ob0ACON-alpha-acetyltransferase 50/0.456
3ntz3TZDihydrofolate reductase1.5.1.30.456
3qwc98PProthrombin3.4.21.50.456
4z5wILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.456
1bjkFADFerredoxin--NADP reductase1.18.1.20.455
1mu6CDAProthrombin3.4.21.50.455
2msdGNPMHC class I alpha chain/0.455
2r6kGTXGlutathione S-transferase A12.5.1.180.455
4bz8J38Histone deacetylase/0.455
4y17LAETranscriptional regulator of ftsQAZ gene cluster/0.455
5dp2NAPCurF/0.455
1h22E10Acetylcholinesterase3.1.1.70.454
1pj6FOLDimethylglycine oxidase1.5.3.100.454
2abaSTRPentaerythritol tetranitrate reductase/0.454
2v3oI26Prothrombin3.4.21.50.454
3hv3R49Mitogen-activated protein kinase 14/0.454
3n71SFGHistone-lysine N-methyltransferase Smyd1/0.454
4hyf1AKTankyrase-22.4.2.300.454
4ifvFMQGag-Pol polyprotein2.7.7.490.454
1a9cGTPGTP cyclohydrolase 13.5.4.160.453
1uzwCDHIsopenicillin N synthase1.21.3.10.453
1vgrCOAFormyl-CoA:oxalate CoA-transferase/0.453
2piaFMNPhthalate dioxygenase reductase/0.453
2vn1FK5Peptidylprolyl isomerase/0.453
3egkM18Prothrombin3.4.21.50.453
3g4gD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.453
3hbfMYCFlavonoid 3-O-glucosyltransferase2.4.10.453
3x1dGDPAtlastin3.6.50.453
3zsgT75Mitogen-activated protein kinase 14/0.453
4fc00T2Serine/threonine-protein kinase B-raf2.7.11.10.453
4qohSTLRibosyldihydronicotinamide dehydrogenase [quinone]/0.453
1n0hCIEAcetolactate synthase catalytic subunit, mitochondrial2.2.1.60.452
1t48BB3Tyrosine-protein phosphatase non-receptor type 13.1.3.480.452
1udtVIAcGMP-specific 3',5'-cyclic phosphodiesterase/0.452
1ypeUIPProthrombin3.4.21.50.452
1z71L17Prothrombin3.4.21.50.452
2wo7ASVIsopenicillin N synthase1.21.3.10.452
2vbpVB1Isopenicillin N synthase1.21.3.10.451
4xbfFADLysine-specific histone demethylase 1A10.451
1kmvLIIDihydrofolate reductase1.5.1.30.450
1yplRA8Prothrombin3.4.21.50.450
2e94364Geranylgeranyl pyrophosphate synthase/0.450
2jh0701Prothrombin3.4.21.50.450
2onfCOAUncharacterized protein/0.450
2w6qOA5Biotin carboxylase6.3.4.140.450
3byzH11Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.450
3hu1AGSTransitional endoplasmic reticulum ATPase3.6.4.60.450
4mm729JNa(+):neurotransmitter symporter (Snf family)/0.450
4tyqAP5Adenylate kinase/0.450
4zzi1NSNAD-dependent protein deacetylase sirtuin-13.5.10.450
1d3pBT3Prothrombin3.4.21.50.449
1e62FADFerredoxin--NADP reductase1.18.1.20.449
2h447CAcGMP-specific 3',5'-cyclic phosphodiesterase/0.449
2w3mFOLDihydrofolate reductase1.5.1.30.449
3hucG97Mitogen-activated protein kinase 14/0.449
3nxyD2HDihydrofolate reductase1.5.1.30.449
3o73O73Ribosyldihydronicotinamide dehydrogenase [quinone]/0.449
4drjRAPSerine/threonine-protein kinase mTOR2.7.11.10.449
4drjRAPPeptidyl-prolyl cis-trans isomerase FKBP45.2.1.80.449
4lzwTHMUridine phosphorylase/0.449
1lnmDTXBilin-binding protein/0.448
2ohhFMNType A flavoprotein FprA10.448
2zfq45UProthrombin3.4.21.50.448
3e6eDCSAlanine racemase/0.448
3gncQQQGlutaryl-CoA dehydrogenase/0.448
3hiiPNTAmiloride-sensitive amine oxidase [copper-containing]/0.448
3w6uNAP6-phosphogluconate dehydrogenase, NAD-binding protein/0.448
4bb2STRCorticosteroid-binding globulin/0.448
4pxzCLRP2Y purinoceptor 12/0.448
5bn3ADPV-type ATP synthase alpha chain/0.448
5bn3ADPNEQ263/0.448
1dgfNDPCatalase1.11.1.60.447
1x1cSAHC-20 methyltransferase/0.447
2r2mI50Prothrombin3.4.21.50.447
3mjrAC2Deoxycytidine kinase2.7.1.740.447
3zk6H1IBcl-2-like protein 1/0.447
4a86H35Major pollen allergen Bet v 1-A/0.447
4bftZVTPantothenate kinase2.7.1.330.447
4feu537Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.447
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.447
1gm7PNNPenicillin G acylase3.5.1.110.446
1pqc444Oxysterols receptor LXR-beta/0.446
1sg0STLRibosyldihydronicotinamide dehydrogenase [quinone]/0.446
1x1dSAHC-20 methyltransferase/0.446
1xagNAD3-dehydroquinate synthase/0.446
2b8jADNClass B acid phosphatase3.1.3.20.446
3bbfGDPNucleoside diphosphate kinase B2.7.4.60.446
3ihzFK5Peptidylprolyl isomerase/0.446
3nhpHGZRibosyldihydronicotinamide dehydrogenase [quinone]/0.446
4a4xJUPSerine/threonine-protein kinase Nek22.7.11.10.446
4az29MUProthrombin3.4.21.50.446
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.446
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.446
4c2jCOA3-ketoacyl-CoA thiolase, mitochondrial2.3.1.160.446
4ey7E20Acetylcholinesterase3.1.1.70.446
4y1bNAPAntE/0.446
1uwhBAXSerine/threonine-protein kinase B-raf2.7.11.10.445
1x1bSAHC-20 methyltransferase/0.445
3c6n2S8Protein TRANSPORT INHIBITOR RESPONSE 1/0.445
3u9y09LTankyrase-22.4.2.300.445
3zloX8UBcl-2-like protein 1/0.445
4bekXK0Beta-secretase 13.4.23.460.445
4jvlESTEstrogen sulfotransferase2.8.2.40.445
4tnzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.445
4x9dU5PUncharacterized protein MJ1435/0.445
5ex0SAHHistone-lysine N-methyltransferase SMYD32.1.1.430.445
5kgjACOPredicted acetyltransferase/0.445
1cl2PPGCystathionine beta-lyase MetC4.4.1.80.444
1dr4HBIDihydrofolate reductase1.5.1.30.444
1j9gFMNFlavodoxin/0.444
1xm1GAHProthrombin3.4.21.50.444
2cn0F25Prothrombin3.4.21.50.444
2hveADPNucleoside diphosphate kinase A2.7.4.60.444
2ydd2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.444
2zsdCOAPantothenate kinase2.7.1.330.444
3dlgGWEGag-Pol polyprotein2.7.7.490.444
3gmd2M3Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.444
3p70ILE_PHE_GLU_PRO_PROProthrombin3.4.21.50.444
3ufl508Beta-secretase 13.4.23.460.444
4i6f1C7Serine/threonine-protein kinase PLK22.7.11.210.444
4qfyDCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.444
5a4vQUEGlutathione S-transferase F22.5.1.180.444
1ex75GPGuanylate kinase2.7.4.80.443
1jg0DDTThymidylate synthase/0.443
1pq944BOxysterols receptor LXR-beta/0.443
2culFADGidA-related protein/0.443
2hkoFADLysine-specific histone demethylase 1A10.443
2z7hGG3Geranylgeranyl pyrophosphate synthase/0.443
3gsiTHGDimethylglycine oxidase1.5.3.100.443
3h4vDVPPteridine reductase 11.5.1.330.443
3lutNAPVoltage-gated potassium channel subunit beta-2/0.443
3uxe465Ribosyldihydronicotinamide dehydrogenase [quinone]/0.443
4a6dSAMAcetylserotonin O-methyltransferase2.1.1.40.443
4b4vL34Bifunctional protein FolD/0.443
4dyn0MRNucleoprotein/0.443
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
4f0e0RUPoly [ADP-ribose] polymerase 152.4.2.300.443
4iwnGEKCarboxy-S-adenosyl-L-methionine synthase/0.443
4ol0GTPGTP-binding nuclear protein Ran/0.443
1rkwPNTHTH-type transcriptional regulator QacR/0.442
1rt9IMHPurine nucleoside phosphorylase2.4.2.10.442
2dw4FADLysine-specific histone demethylase 1A10.442
2hvdADPNucleoside diphosphate kinase A2.7.4.60.442
2zfr46UProthrombin3.4.21.50.442
2znk31UProthrombin3.4.21.50.442
3szfDCQSulfide-quinone reductase/0.442
4c6zTLE3-oxoacyl-ACP synthase/0.442
4kfqKFQGlutamate receptor ionotropic, NMDA 1/0.442
4omaLCSMethionine gamma-lyase/0.442
4xnhACON-terminal acetyltransferase A complex subunit NAT52.3.10.442
5c80URIUridine phosphorylase/0.442
1dhfFOLDihydrofolate reductase1.5.1.30.441
1odcA8BAcetylcholinesterase3.1.1.70.441
1r8qAFBCytohesin-2/0.441
1r8qAFBADP-ribosylation factor 1/0.441
2b5oFADFerredoxin--NADP reductase1.18.1.20.441
2bfaCB3Pteridine reductase 11.5.1.330.441
2bvs2CEProthrombin3.4.21.50.441
3b8xG4MPutative pyridoxamine 5-phosphate-dependent dehydrase/0.441
3n3aFMNProtein NrdI/0.441
3nwlNDPCatalase1.11.1.60.441
3qeoLLTDeoxycytidine kinase2.7.1.740.441
4c717RD3-oxoacyl-ACP synthase/0.441
4gr9372Ribosyldihydronicotinamide dehydrogenase [quinone]/0.441
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.441
4mmc29JNa(+):neurotransmitter symporter (Snf family)/0.441
4nbiD3YD-tyrosyl-tRNA(Tyr) deacylase/0.441
4to2DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.441
1d3dBZTProthrombin3.4.21.50.440
1d6w00RProthrombin3.4.21.50.440
1o6qR17Squalene--hopene cyclase4.2.1.1290.440
1pl6572Sorbitol dehydrogenase1.1.1.140.440
1tllFADNitric oxide synthase, brain1.14.13.390.440
1w1wAGSStructural maintenance of chromosomes protein 1/0.440
2dxdANPNucleoside diphosphate kinase2.7.4.60.440
2pbwDOQGlutamate receptor ionotropic, kainate 1/0.440
2qe2452Polyprotein/0.440
2ql6TIZNicotinamide riboside kinase 1/0.440
2vd0D27Hematopoietic prostaglandin D synthase/0.440
2vqqTFGHistone deacetylase 43.5.1.980.440
3dmhSAMProbable ribosomal RNA small subunit methyltransferase/0.440
3nu03TUDihydrofolate reductase1.5.1.30.440
4af7FADFerredoxin--NADP reductase, leaf isozyme, chloroplastic1.18.1.20.440
4wbdADPPutative cysteine ligase BshC/0.440
5agyGTBTau class glutathione S-transferase/0.440
5cc9DDFDihydrofolate reductase1.5.1.30.440