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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
3nhuM42Ribosyldihydronicotinamide dehydrogenase [quinone]

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
3nhuM42Ribosyldihydronicotinamide dehydrogenase [quinone]/1.000
3nhpHGZRibosyldihydronicotinamide dehydrogenase [quinone]/0.703
3nhjA2ZRibosyldihydronicotinamide dehydrogenase [quinone]/0.655
3o73O73Ribosyldihydronicotinamide dehydrogenase [quinone]/0.642
3nhyA7BRibosyldihydronicotinamide dehydrogenase [quinone]/0.637
3uxe465Ribosyldihydronicotinamide dehydrogenase [quinone]/0.632
4gqiM49Ribosyldihydronicotinamide dehydrogenase [quinone]/0.627
3uxhUXHRibosyldihydronicotinamide dehydrogenase [quinone]/0.625
3nhfVVVRibosyldihydronicotinamide dehydrogenase [quinone]/0.624
3owxXRARibosyldihydronicotinamide dehydrogenase [quinone]/0.620
2bzsCB1Ribosyldihydronicotinamide dehydrogenase [quinone]/0.612
4fgj1PQRibosyldihydronicotinamide dehydrogenase [quinone]/0.611
1sg0STLRibosyldihydronicotinamide dehydrogenase [quinone]/0.608
3nhkVAPRibosyldihydronicotinamide dehydrogenase [quinone]/0.605
3ox34X4Ribosyldihydronicotinamide dehydrogenase [quinone]/0.602
4zvmDM2Ribosyldihydronicotinamide dehydrogenase [quinone]/0.601
3ox279XRibosyldihydronicotinamide dehydrogenase [quinone]/0.592
3ox1695Ribosyldihydronicotinamide dehydrogenase [quinone]/0.591
3nhlYTRRibosyldihydronicotinamide dehydrogenase [quinone]/0.590
4gr9372Ribosyldihydronicotinamide dehydrogenase [quinone]/0.590
2qmzLDPRibosyldihydronicotinamide dehydrogenase [quinone]/0.576
3nfrEWQRibosyldihydronicotinamide dehydrogenase [quinone]/0.576
3nhwZXZRibosyldihydronicotinamide dehydrogenase [quinone]/0.575
1xi2CB1Ribosyldihydronicotinamide dehydrogenase [quinone]/0.574
3gamMXXRibosyldihydronicotinamide dehydrogenase [quinone]/0.551
1zx1CB1Ribosyldihydronicotinamide dehydrogenase [quinone]/0.547
4qohSTLRibosyldihydronicotinamide dehydrogenase [quinone]/0.546
3nhrRZWRibosyldihydronicotinamide dehydrogenase [quinone]/0.531
4dymIYZActivin receptor type-12.7.11.300.508
4qofFMNRibosyldihydronicotinamide dehydrogenase [quinone]/0.504
3g5mFADRibosyldihydronicotinamide dehydrogenase [quinone]/0.503
1o5rFR9Adenosine deaminase3.5.4.40.479
2bktRPFRenin3.4.23.150.478
3clxX22E3 ubiquitin-protein ligase XIAP6.3.20.478
4qoeFADRibosyldihydronicotinamide dehydrogenase [quinone]/0.478
1sjwNGVNogalonic acid methyl ester cyclase/0.477
3arvSAUChitinase A/0.476
3v94WYQPhosphodiesterase/0.476
1umlFR4Adenosine deaminase3.5.4.40.475
2fs4PZ1Renin3.4.23.150.475
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.475
3w78CBDFMN-dependent NADH-azoreductase/0.475
3t8vBTJM1 family aminopeptidase3.4.110.474
4aojV4ZHigh affinity nerve growth factor receptor2.7.10.10.473
5ckwANPUncharacterized protein/0.473
1vrqFONSubunit alpha of sarocosine oxidase/0.472
3dmjGWEPol protein/0.472
3fu83DMLaccase-11.10.3.20.471
4zvlFADRibosyldihydronicotinamide dehydrogenase [quinone]/0.471
2zozETTranscriptional regulator/0.470
4pkl1GHUncharacterized protein/0.470
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.469
4i9z5BAcGMP-specific 3',5'-cyclic phosphodiesterase/0.468
2nmtMIMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.467
4jib1L6cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.467
2xytTC9Soluble acetylcholine receptor/0.466
3b9lAZZSerum albumin/0.466
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.466
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.466
4c2z646Glycylpeptide N-tetradecanoyltransferase 1/0.466
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.466
5fd8A5APutative carboxypeptidase yocD/0.463
1nquRDL6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.462
2f98NGVAklanonic acid methyl ester cyclase AcmA5.5.1.230.462
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.462
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.461
2ojg19AMitogen-activated protein kinase 12.7.11.240.461
2xtbKRMAdenosine kinase, putative/0.461
3arpDEQChitinase A/0.461
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.461
3s7a684Dihydrofolate reductase1.5.1.30.461
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.461
1qxlFR8Adenosine deaminase3.5.4.40.460
3o9lLPNRenin3.4.23.150.460
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.460
4lm5Q17Serine/threonine-protein kinase pim-12.7.11.10.460
1disBDMDihydrofolate reductase1.5.1.30.459
1ndzFR5Adenosine deaminase3.5.4.40.459
2h447CAcGMP-specific 3',5'-cyclic phosphodiesterase/0.459
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.459
4gtv7TRGeranylgeranyl transferase type-2 subunit beta2.5.1.600.458
1v7aFRCAdenosine deaminase3.5.4.40.457
2wsa646Glycylpeptide N-tetradecanoyltransferase/0.457
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.457
3pm1ETHTH-type transcriptional regulator QacR/0.457
4a322CDGlycylpeptide N-tetradecanoyltransferase/0.457
4iaq2GM5-hydroxytryptamine receptor 1B/0.457
4qa0SHHHistone deacetylase 83.5.1.980.457
1s3uTQDDihydrofolate reductase1.5.1.30.456
3g6zA7TRenin3.4.23.150.456
4yauFADNADPH--cytochrome P450 reductase/0.456
5bn3ADPV-type ATP synthase alpha chain/0.456
5bn3ADPNEQ263/0.456
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.455
3br3ETHTH-type transcriptional regulator QacR/0.455
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
3kozZ97D-ornithine 4,5-aminomutase subunit beta/0.455
3sl6JN8cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.455
3zs5SB2Mitogen-activated protein kinase 14/0.455
3adaNADSubunit alpha of sarocosine oxidase/0.454
3bgqVX2Serine/threonine-protein kinase pim-12.7.11.10.454
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
3nxvD2FDihydrofolate reductase1.5.1.30.454
3oagLPQRenin3.4.23.150.454
3sl8JN7cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.454
4amjCVDBeta-1 adrenergic receptor/0.454
1e8zSTUPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.453
1pd9CO4Dihydrofolate reductase1.5.1.30.453
3qi4IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
3udq09EBeta-secretase 13.4.23.460.453
4bvnP32Beta-1 adrenergic receptor/0.453
4ey6GNTAcetylcholinesterase3.1.1.70.453
4qa2SHHHistone deacetylase 83.5.1.980.453
1s3vTQDDihydrofolate reductase1.5.1.30.452
1uy6PU3Heat shock protein HSP 90-alpha/0.452
3fu9KIBLaccase-11.10.3.20.452
3gwfFADCyclohexanone monooxygenase/0.452
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
5bp9SAHPutative methyltransferase protein/0.452
5d7q4I5NAD-dependent protein deacetylase sirtuin-23.5.10.452
2c9dPHR6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.451
2cx8SAHRibosomal RNA small subunit methyltransferase E/0.451
3ssnMVIMycinamicin VI 2''-O-methyltransferase/0.451
4a2zVIQGlycylpeptide N-tetradecanoyltransferase/0.451
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.451
4qg0DUTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.451
2cleF6FTryptophan synthase alpha chain/0.450
2yac937Serine/threonine-protein kinase PLK12.7.11.210.450
4jvmXDIEstrogen sulfotransferase2.8.2.40.450
4nt3ZAWLactoperoxidase1.11.1.70.450
4y7cFADNADPH--cytochrome P450 reductase/0.450
1zdwFLVPrenyltransferase/0.449
2rl52RLVascular endothelial growth factor receptor 22.7.10.10.449
2zjmF1MBeta-secretase 13.4.23.460.449
3l9nL9NcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.449
3q44D50M1 family aminopeptidase3.4.110.449
4bbxLKFcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.449
4i8vBHFCytochrome P450 1A11.14.14.10.449
1kl2FONSerine hydroxymethyltransferase/0.448
2nnqT4BFatty acid-binding protein, adipocyte/0.448
3g58988cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.448
3pqbVGPPutative oxidoreductase/0.448
3q3cNADNAD-dependent L-serine dehydrogenase/0.448
3qgtCP6Bifunctional dihydrofolate reductase-thymidylate synthase/0.448
3v0p4GWHisto-blood group ABO system transferase/0.448
4dbs0HVAldo-keto reductase family 1 member C3/0.448
4eufNADTrans-2-enoyl-CoA reductase [NADH]/0.448
4to2DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.448
1kuyCOTSerotonin N-acetyltransferase/0.447
2b82ADNClass B acid phosphatase3.1.3.20.447
2c42TPPPyruvate synthase/0.447
2gjnFMNNitronate monooxygenase1.13.12.160.447
3g70A5TRenin3.4.23.150.447
4egnTWOCytochrome P450/0.447
4h3j10WBeta-secretase 13.4.23.460.447
4oacADPProtein BRASSINOSTEROID INSENSITIVE 12.7.10.10.447
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.446
1qr2FADRibosyldihydronicotinamide dehydrogenase [quinone]/0.446
1vkgCRIHistone deacetylase 83.5.1.980.446
2jdvL20cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.446
3bw4FMNPutative 2-nitropropane dioxygenase/0.446
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3ielU5PRibonuclease TTHA02523.10.446
3ix4TX1Transcriptional activator protein LasR/0.446
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3w5eNVWcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.446
4rxqDUTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.446
4tnzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.446
1hb3SCVIsopenicillin N synthase1.21.3.10.445
1lf2R37Plasmepsin-23.4.23.390.445
1mvtDTMDihydrofolate reductase1.5.1.30.445
1rtiHEFGag-Pol polyprotein2.7.7.490.445
1s9dAFBCytohesin-2/0.445
1s9dAFBADP-ribosylation factor 1/0.445
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.445
2bf4FMNNADPH--cytochrome P450 reductase/0.445
2in6839Wee1-like protein kinase2.7.10.20.445
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
3pz3PZ3Geranylgeranyl transferase type-2 subunit beta2.5.1.600.445
3v0o4GWHisto-blood group ABO system transferase/0.445
4b6l9ZPSerine/threonine-protein kinase PLK32.7.11.210.445
4bchT7ZCyclin-dependent kinase 92.7.11.220.445
5ao1DG3Deoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.445
5d6lCAUBeta-2 adrenergic receptor/0.445
1dibL34C-1-tetrahydrofolate synthase, cytoplasmic1.5.1.50.444
1e8xATPPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
1u1d181Uridine phosphorylase2.4.2.30.444
3q5pTACMultidrug-efflux transporter 1 regulator/0.444
3qfrFADNADPH--cytochrome P450 reductase/0.444
3u8hBHPPhospholipase A2, membrane associated/0.444
3wd9QPCcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.444
4cax646Glycylpeptide N-tetradecanoyltransferase2.3.1.970.444
4hni16WCasein kinase I isoform epsilon2.7.11.10.444
4zweDGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.444
1gzuNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.443
1mczTDPBenzoylformate decarboxylase4.1.1.70.443
1tl7ONMAdenylate cyclase type 2/0.443
1tl7ONMAdenylate cyclase type 5/0.443
1u1cBAUUridine phosphorylase2.4.2.30.443
1v79FR7Adenosine deaminase3.5.4.40.443
1z6tADPApoptotic protease-activating factor 1/0.443
2j9gANPBiotin carboxylase6.3.4.140.443
3e5aVX6Aurora kinase A2.7.11.10.443
3gieACPSensor histidine kinase DesK2.7.13.30.443
3hxbBD5Geranylgeranyl transferase type-2 subunit beta2.5.1.600.443
3koyZ97D-ornithine 4,5-aminomutase subunit beta/0.443
4da7AC2Purine nucleoside phosphorylase DeoD-type2.4.2.10.443
5j60FADThioredoxin reductase/0.443
4amiG90Beta-1 adrenergic receptor/0.443
1diuBDMDihydrofolate reductase1.5.1.30.442
1jtuLYBThymidylate synthase/0.442
1r2jFADFkbI/0.442
1tu8GTXGlutathione S-transferase 22.5.1.180.442
2w6mOA1Biotin carboxylase6.3.4.140.442
3o57ZG2cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.442
3tifADPUncharacterized ABC transporter ATP-binding protein MJ0796/0.442
4eilFOLBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.442
4fj2QSO17beta-hydroxysteroid dehydrogenase/0.442
4iarERM5-hydroxytryptamine receptor 1B/0.442
4jlj1NMDeoxycytidine kinase2.7.1.740.442
4qfzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.442
4rbs0RVMetallo-beta-lactamase type 2/0.442
4to1DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.442
1blzACVIsopenicillin N synthase1.21.3.10.441
1digL37C-1-tetrahydrofolate synthase, cytoplasmic1.5.1.50.441
1h66RH1NAD(P)H dehydrogenase [quinone] 11.6.5.20.441
1h69ARHNAD(P)H dehydrogenase [quinone] 11.6.5.20.441
1kziTHGThymidylate synthase/0.441
1odcA8BAcetylcholinesterase3.1.1.70.441
2jb4A14Isopenicillin N synthase1.21.3.10.441
2oymMNIEndoglycoceramidase II/0.441
2v16C47Renin3.4.23.150.441
2v57PRLTetR family transcriptional regulator/0.441
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3ha5SFGHydroxymycolate synthase MmaA42.1.10.441
3ojxFMNNADPH--cytochrome P450 reductase/0.441
4ddrMMVDihydrofolate reductase1.5.1.30.441
4rxsTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.441
5a4vQUEGlutathione S-transferase F22.5.1.180.441
2rh1CAUBeta-2 adrenergic receptor/0.441
1bozPRDDihydrofolate reductase1.5.1.30.440
1dgbNDPCatalase1.11.1.60.440
1i2lDCSAminodeoxychorismate lyase4.1.3.380.440
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
1obnASVIsopenicillin N synthase1.21.3.10.440
2j9lATPH(+)/Cl(-) exchange transporter 5/0.440
2x9dITCTetracycline repressor protein class D/0.440
2zevB71Geranylgeranyl pyrophosphate synthase/0.440
3g4gD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
3iakEV1cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
3u5sFADFAD-linked sulfhydryl oxidase ALR1.8.3.20.440
4rxpDTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.440
2ycyP32Beta-1 adrenergic receptor/0.440