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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
3uthGDUUDP-galactopyranose mutase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3uthGDUUDP-galactopyranose mutase/1.000
4u8jFDAUDP-galactopyranose mutase/0.545
2a5hSAML-lysine 2,3-aminomutase5.4.3.20.502
2anb5GPGuanylate kinase2.7.4.80.490
3intGDUUDP-galactopyranose mutase5.4.99.90.485
3fccATPD-alanine--poly(phosphoribitol) ligase subunit 1/0.482
3vjlW94Dipeptidyl peptidase 4/0.482
3tr05GPGuanylate kinase/0.481
2pj4414Carboxypeptidase B/0.480
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.479
3intFDAUDP-galactopyranose mutase5.4.99.90.477
4qg1DTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.475
1u1gBBBUridine phosphorylase2.4.2.30.474
1dfoPLGSerine hydroxymethyltransferase2.1.2.10.473
2vatCOAAcetyl-CoA--deacetylcephalosporin C acetyltransferase2.3.1.1750.473
3q8uADPNucleoside diphosphate kinase/0.473
3vjkM51Dipeptidyl peptidase 4/0.472
4c13UMLUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase/0.472
3fr5I4AFatty acid-binding protein, adipocyte/0.470
1foaUD1Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase2.4.1.1010.469
3c1kT15Prothrombin3.4.21.50.469
1u1f183Uridine phosphorylase2.4.2.30.468
2ixkTDOdTDP-4-dehydrorhamnose 3,5-epimerase5.1.3.130.468
3hdyGDUUDP-galactopyranose mutase/0.468
4yaw2AMNADPH--cytochrome P450 reductase/0.468
3ccc7ACDipeptidyl peptidase 4/0.467
3elbC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.467
2f3rG5PGuanylate kinase2.7.4.80.466
5cnsDATRibonucleoside-diphosphate reductase 1 subunit alpha1.17.4.10.466
2ea2F77Methionine aminopeptidase 2/0.465
3opmLUIDipeptidyl peptidase 4/0.465
1ds7FMNOxygen-insensitive NAD(P)H nitroreductase/0.464
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.464
4fljY08Methionine aminopeptidase 1/0.464
3qbjNXZDipeptidyl peptidase 4/0.463
1pqc444Oxysterols receptor LXR-beta/0.462
3fceATPD-alanine--poly(phosphoribitol) ligase subunit 1/0.462
4u0sADPAdenosine monophosphate-protein transferase FICD2.7.7.n10.462
4zzi1NSNAD-dependent protein deacetylase sirtuin-13.5.10.462
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.461
2vf3GVS4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.460
1akaPLPAspartate aminotransferase, mitochondrial2.6.1.10.459
1ylrFMNOxygen-insensitive NAD(P)H nitroreductase/0.459
3hf3FMNChromate reductase/0.459
3nubUD0UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.459
3zgz84TLeucine--tRNA ligase/0.459
4gdcNDPUDP-galactopyranose mutase/0.459
4ycoFMNtRNA-dihydrouridine(16) synthase/0.459
1qbqHFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.458
1qbqHFPProtein farnesyltransferase subunit beta2.5.1.580.458
1s4oGDPGlycolipid 2-alpha-mannosyltransferase/0.458
3uzxAOX3-oxo-5-beta-steroid 4-dehydrogenase/0.458
1lkdBP6Biphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.457
1nhkCMPNucleoside diphosphate kinase2.7.4.60.457
3hdqGDUUDP-galactopyranose mutase/0.457
3mj4URMUDP-galactopyranose mutase/0.457
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.457
5kwvANPPantothenate synthetase/0.457
1gtrATPGlutamine--tRNA ligase6.1.1.180.456
2xyd3ESAngiotensin-converting enzyme3.2.10.456
3skgPB8Beta-secretase 13.4.23.460.456
4bcdTDVProlyl endopeptidase3.4.21.260.456
4loh1SYStimulator of interferon genes protein/0.456
1nzdUPGDNA beta-glucosyltransferase/0.455
2xiq5ADMethylmalonyl-CoA mutase, mitochondrial/0.455
3m2uCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.455
3wqmB29Diterpene synthase3.1.7.80.455
4kp71UQ1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic1.1.1.2670.455
4qfzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.455
1n95HFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.454
1n95HFPProtein farnesyltransferase subunit beta2.5.1.580.454
2abaSTRPentaerythritol tetranitrate reductase/0.454
2eixFADNADH-cytochrome b5 reductase/0.454
3apwDP0Alpha-1-acid glycoprotein 2/0.454
3td7FADProbable FAD-linked sulfhydryl oxidase R5961.8.3.20.454
4ikzAFSDi-tripeptide ABC transporter (Permease)/0.454
4loi1YCStimulator of interferon genes protein/0.454
2c6c24IGlutamate carboxypeptidase 23.4.17.210.453
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.453
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.453
3fx6BPXCarboxypeptidase A13.4.17.10.453
3v0o4GWHisto-blood group ABO system transferase/0.453
4dptAGSMevalonate diphosphate decarboxylase/0.453
5bnw12VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.453
1wamFADUDP-galactopyranose mutase5.4.99.90.452
1z48FMNNADPH dehydrogenase/0.452
2hs6FMN12-oxophytodienoate reductase 31.3.1.420.452
2iko7IGRenin3.4.23.150.452
2r8fAGSNon-structural protein 23.6.40.452
4bfzZVZPantothenate kinase2.7.1.330.452
4tnzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.452
1i5bANPChemotaxis protein CheA2.7.13.30.451
1mbbEEBUDP-N-acetylenolpyruvoylglucosamine reductase1.3.1.980.451
1p4aPCPPur operon repressor/0.451
1q20PLOSulfotransferase family cytosolic 2B member 12.8.2.20.451
1wklATPNucleoside diphosphate kinase/0.451
1zioAP5Adenylate kinase/0.451
2f3mGTDGlutathione S-transferase Mu 12.5.1.180.451
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.451
2rgu356Dipeptidyl peptidase 4/0.451
2v5aLZLBiotin carboxylase6.3.4.140.451
1nj6A5AProline--tRNA ligase/0.450
2q1uNADPutative nucleotide sugar epimerase/ dehydratase/0.450
3lm8VIBThiamine pyrophosphokinase2.7.6.20.450
3lpiZ74Beta-secretase 13.4.23.460.450
3m1vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.450
3m1vCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.450
3nzpPLPArginine decarboxylase/0.450
3pkbY16Methionine aminopeptidase 2/0.450
4qfyDCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.450
4tyqAP5Adenylate kinase/0.450
1ni12C5Protein farnesyltransferase subunit beta2.5.1.580.449
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.449
2rds1PL1-deoxypentalenic acid 11-beta-hydroxylase1.14.11.350.449
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3fr4F8AFatty acid-binding protein, adipocyte/0.449
1a9zUPGUDP-glucose 4-epimerase5.1.3.20.448
1eyyNAPNADP-dependent fatty aldehyde dehydrogenase1.2.1.40.448
1h6cNDPGlucose--fructose oxidoreductase1.1.99.280.448
1taeNADDNA ligase/0.448
4b64FADL-ornithine N(5)-monooxygenase/0.448
4l0oPLPCystathionine gamma-synthase2.5.1.480.448
2af6FADFlavin-dependent thymidylate synthase2.1.1.1480.447
2fxv5GPXanthine phosphoribosyltransferase2.4.2.220.447
2hwuURIUridine phosphorylase2.4.2.30.447
2q96A18Methionine aminopeptidase/0.447
2zdyADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.447
3axkNDPRibulose bisphosphate carboxylase large chain4.1.1.390.447
3eu5GBOProtein farnesyltransferase subunit beta2.5.1.580.447
3f8sPF2Dipeptidyl peptidase 4/0.447
3g0bT22Dipeptidyl peptidase 4/0.447
3lqsPSZD-alanine aminotransferase2.6.1.210.447
3u9eCOALmo1369 protein/0.447
4hyvPEPPyruvate kinase 12.7.1.400.447
1ni1HFPProtein farnesyltransferase subunit beta2.5.1.580.446
1tcoFK5Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.446
1tcoFK5Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform3.1.3.160.446
2h3wHC5Carnitine O-acetyltransferase2.3.1.70.446
2wzySQXSoluble acetylcholine receptor/0.446
3dr7GPDGDP-perosamine synthase/0.446
3hl4CDCCholine-phosphate cytidylyltransferase A/0.446
3lnc5GPGuanylate kinase/0.446
3ukfGDUUDP-galactopyranose mutase/0.446
4a1oAMZBifunctional purine biosynthesis protein PurH2.1.2.30.446
4de00JBBeta-lactamase/0.446
4k8s1QTBeta-secretase 13.4.23.460.446
1lc3NADBiliverdin reductase A1.3.1.240.445
1nj5P5AProline--tRNA ligase/0.445
1towCRZFatty acid-binding protein, adipocyte/0.445
2qimZEAClass 10 plant pathogenesis-related protein/0.445
3aezGDPPantothenate kinase2.7.1.330.445
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
4fkzUD1UDP-N-acetylglucosamine 2-epimerase5.1.3.140.445
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.445
4rxqDUTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.445
1gky5GPGuanylate kinase2.7.4.80.444
1oxoIK2Aspartate aminotransferase, mitochondrial2.6.1.10.444
2b3dFADModulator of drug activity B/0.444
2dxdANPNucleoside diphosphate kinase2.7.4.60.444
2q1tNADPutative nucleotide sugar epimerase/ dehydratase/0.444
2zueANPArginine--tRNA ligase6.1.1.190.444
3m30COMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.444
3m30COMMethyl-coenzyme M reductase I subunit beta2.8.4.10.444
4cf6CBDNAD(P)H dehydrogenase [quinone] 11.6.5.20.444
1b5eDCMDeoxycytidylate 5-hydroxymethyltransferase2.1.2.80.443
1necFMNOxygen-insensitive NAD(P)H nitroreductase10.443
1nl4HFPProtein farnesyltransferase subunit beta2.5.1.580.443
1xvaSAMGlycine N-methyltransferase2.1.1.200.443
2nnqT4BFatty acid-binding protein, adipocyte/0.443
2x90EALAngiotensin-converting enzyme3.4.15.10.443
3g0cRUFDipeptidyl peptidase 4/0.443
3p3c3P3UDP-3-O-acyl-N-acetylglucosamine deacetylase/0.443
4dbc3QPAspartate aminotransferase2.6.1.10.443
4fllYZ6Methionine aminopeptidase 1/0.443
4jb1NAPUDP-N-acetylenolpyruvoylglucosamine reductase/0.443
1s4pGDPGlycolipid 2-alpha-mannosyltransferase/0.442
1vfrFMNMajor NAD(P)H-flavin oxidoreductase1.6.990.442
1x2bSTXProline iminopeptidase3.4.11.50.442
2g1y5IGRenin3.4.23.150.442
3ei8PL5LL-diaminopimelate aminotransferase, chloroplastic/0.442
3m2vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.442
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.442
4h9tHL4Phosphotriesterase/0.442
4o30SAHProbable Histone-lysine N-methyltransferase ATXR52.1.1.430.442
4pryLEU_GLU_THR_ACE_ASACaspase-33.4.22.560.442
4uz6SCRPalmitoleoyl-protein carboxylesterase NOTUM/0.442
5c80URIUridine phosphorylase/0.442
1jedADPSulfate adenylyltransferase/0.441
1kh3ANPArgininosuccinate synthase/0.441
1nqw5YL6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.441
1r5gAO1Methionine aminopeptidase 2/0.441
2pakTYDTDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase5.3.2.30.441
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
4b2gV1NUncharacterized protein/0.441
4bf9FMNtRNA-dihydrouridine(16) synthase/0.441
4w5kPLPAspartate aminotransferase, mitochondrial/0.441
1lvg5GPGuanylate kinase2.7.4.80.440
1n95FTHProtein farnesyltransferase subunit beta2.5.1.580.440
1ykiFMNOxygen-insensitive NAD(P)H nitroreductase/0.440
2pzjNADPutative nucleotide sugar epimerase/ dehydratase/0.440
2whqHI6Acetylcholinesterase3.1.1.70.440
3g0gRUMDipeptidyl peptidase 4/0.440
4g1f0WGDipeptidyl peptidase 4/0.440
4lzwTHMUridine phosphorylase/0.440
4p5bFADFlavin-dependent thymidylate synthase/0.440