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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
4nu6NADPhosphonate dehydrogenase1.20.1.1

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
4nu6NADPhosphonate dehydrogenase1.20.1.11.000
4nu5NADPhosphonate dehydrogenase1.20.1.10.613
4e5nNADPhosphonate dehydrogenase1.20.1.10.562
4e5kNADPhosphonate dehydrogenase1.20.1.10.557
2w2lNADD-mandelate dehydrogenase/0.537
2dbzNAPGlyoxylate reductase1.1.1.260.521
4e5mNAPPhosphonate dehydrogenase1.20.1.10.515
1sn5T3Transthyretin/0.493
3kb6NADD-lactate dehydrogenase/0.491
2yfeYFEPeroxisome proliferator-activated receptor gamma/0.490
1oiyN41Cyclin-dependent kinase 22.7.11.220.489
3oibFDAPutative acyl-CoA dehydrogenase/0.479
2xvu9DNSerum albumin/0.478
2j3kNAPNADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.475
5j23A2RPutative 2-hydroxyacid dehydrogenase/0.475
1ai9NDPDihydrofolate reductase1.5.1.30.474
4ly91YYGlucokinase regulatory protein/0.474
1mg5NAIAlcohol dehydrogenase1.1.1.10.473
2w9sTOPDihydrofolate reductase type 1 from Tn40031.5.1.30.473
4wuoNAD3-isopropylmalate dehydrogenase1.1.1.850.473
3bazNAPHydroxyphenylpyruvate reductase1.1.1.2370.472
1ie8KH1Vitamin D3 receptor/0.470
1oc1ASVIsopenicillin N synthase1.21.3.10.470
2j3iNAPNADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.470
3ml8ML8Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.470
4jbiNDPAlcohol dehydrogenase (Zinc)/0.470
4z44FADFlavin-dependent tryptophan halogenase PrnA1.14.19.90.470
1wwkNAD307aa long hypothetical phosphoglycerate dehydrogenase/0.469
3hz5Z64Heat shock protein HSP 90-alpha/0.469
3ssnMVIMycinamicin VI 2''-O-methyltransferase/0.469
3vrwYS5Vitamin D3 receptor/0.469
5bqfNAPProbable hydroxyacid dehydrogenase protein/0.469
2eklNADD-3-phosphoglycerate dehydrogenase/0.468
4q72FADBifunctional protein PutA/0.468
4y9lFADAcyl-CoA dehydrogenase family member 11/0.468
1uzwCDHIsopenicillin N synthase1.21.3.10.467
2b9wFADPutative aminooxidase/0.467
3f46I2C5,10-methenyltetrahydromethanopterin hydrogenase1.12.98.20.467
4q73FADBifunctional protein PutA/0.466
1ay0TPPTransketolase 12.2.1.10.465
1qvnFRIInterleukin-2/0.465
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.465
2g9uG27Glycogen phosphorylase, muscle form2.4.1.10.465
3jynNDPQuinone oxidoreductase/0.465
3t1tGDPProbable gliding protein mglA/0.465
3vt9YI4Vitamin D3 receptor/0.465
4xcvNDPProbable hydroxyacid dehydrogenase protein/0.465
4xgxADPFAD:protein FMN transferase/0.465
1tehNADAlcohol dehydrogenase class-31.1.1.10.464
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.464
1w2xRCPAcetyl-CoA carboxylase/0.463
2bu9HFVIsopenicillin N synthase1.21.3.10.463
3kjrNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.463
4z0pNDPNAD-dependent dehydrogenase/0.463
2rghFADAlpha-Glycerophosphate Oxidase/0.462
2y05NAPProstaglandin reductase 1/0.462
3ge1ADPGlycerol kinase/0.462
3qlrNDPDihydrofolate reductase1.5.1.30.462
3sgtP09Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)/0.462
3t14FADSulfide-quinone reductase/0.462
3t2kFADSulfide-quinone reductase/0.462
3v8w0G2Tyrosine-protein kinase ITK/TSK2.7.10.20.462
4a4wYFBPeroxisome proliferator-activated receptor gamma/0.462
4z3dNDPCarbonyl reductase [NADPH] 11.1.1.1840.462
1gqtACPRibokinase/0.461
1w06W05Isopenicillin N synthase1.21.3.10.461
2zb3NDPProstaglandin reductase 21.3.1.480.461
3qk0QK0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.461
3rwpABQ3-phosphoinositide-dependent protein kinase 12.7.11.10.461
4fc7NAPPeroxisomal 2,4-dienoyl-CoA reductase1.3.1.340.461
1nzdUPGDNA beta-glucosyltransferase/0.460
2dbqNAPGlyoxylate reductase1.1.1.260.460
2gjlFMNNitronate monooxygenase1.13.12.160.460
4gb90WRPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.460
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.459
2p9cNAID-3-phosphoglycerate dehydrogenase1.1.1.950.459
2qg2A91Heat shock protein HSP 90-alpha/0.459
3lpkZ76Beta-secretase 13.4.23.460.458
4mihFADPyranose 2-oxidase1.1.3.100.458
1hkuNADC-terminal-binding protein 11.1.10.457
1ppjANYCytochrome b/0.457
2pa3NAID-3-phosphoglycerate dehydrogenase1.1.1.950.457
2vbdV10Isopenicillin N synthase1.21.3.10.457
3h0sB38Acetyl-CoA carboxylase/0.457
3iaeD7KBenzaldehyde lyase/0.457
3kpkFADSulfide-quinone reductase/0.457
3w5tLHPVitamin D3 receptor/0.457
1g4tFTPThiamine-phosphate synthase/0.456
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.456
1k6cMK1Gag-Pol polyprotein3.4.23.160.456
2g5cNADPrephenate dehydrogenase/0.456
2q4bNAPUncharacterized protein At5g02240/0.456
2tpsTPSThiamine-phosphate synthase/0.456
3tqhNDPQuinone oxidoreductase/0.456
4q71FADBifunctional protein PutA/0.456
1yb5NAPQuinone oxidoreductase1.6.5.50.455
3h4lANPDNA mismatch repair protein PMS1/0.455
3vt65YIVitamin D3 receptor/0.455
3vtdTKDVitamin D3 receptor/0.455
4rpjFADUDP-galactopyranose mutase5.4.99.90.455
2ft9CHDFatty acid-binding protein 2, liver/0.454
2gcgNDPGlyoxylate reductase/hydroxypyruvate reductase1.1.1.790.454
2hb8MVDVitamin D3 receptor/0.454
3jzdNADMaleylacetate reductase/0.454
3vt5YI2Vitamin D3 receptor/0.454
4cy8FDA2-hydroxybiphenyl-3-monooxygenase/0.454
5k2aZMAAdenosine receptor A2a/0.454
1qp8NDP2-hydroxyacid dehydrogenase/0.453
2hbhXE4Vitamin D3 receptor A/0.453
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.453
3mkhFADNitroalkane oxidase/0.453
3t2zFADSulfide-quinone reductase/0.453
3vetADPnebramycin 5' synthase6.1.2.20.453
4e37NDPCatalase1.11.1.60.453
4ia3BIVVitamin D3 receptor A/0.453
1kzjCB3Thymidylate synthase/0.452
2harOCCVitamin D3 receptor/0.452
2ykeYKEHeat shock protein HSP 90-alpha/0.452
4hbm0Y7E3 ubiquitin-protein ligase Mdm26.3.20.452
1ictT44Transthyretin/0.451
1ipeNDPTropinone reductase 21.1.1.2360.451
1szmBI4cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.451
2bx8AZQSerum albumin/0.451
2q4wFADCytokinin dehydrogenase 71.5.99.120.451
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.451
2vnaNAPProstaglandin reductase 21.3.1.480.451
2zafFADNitroalkane oxidase1.7.3.10.451
3dafFEG5,10-methenyltetrahydromethanopterin hydrogenase1.12.98.20.451
3f47I2C5,10-methenyltetrahydromethanopterin hydrogenase1.12.98.20.451
3p2eSAH16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.451
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.451
5eoxADPType 4 fimbrial biogenesis protein PilM/0.451
1jioDEB6-deoxyerythronolide B hydroxylase/0.450
1o8cNDPProbable acrylyl-CoA reductase AcuI1.3.1.840.450
1t0lNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.450
2iyaZIOOleandomycin glycosyltransferase/0.450
2qa2FADPolyketide oxygenase CabE/0.450
2ww4ADP4-diphosphocytidyl-2-C-methyl-D-erythritol kinase2.7.1.1480.450
2ydfIO3Serum albumin/0.450
3adaNADSubunit alpha of sarocosine oxidase/0.450
3lu8IQXSerum albumin/0.450
3oroAGSSerine/threonine protein kinase/0.450
3vt7VDXVitamin D3 receptor/0.450
5k2bZMAAdenosine receptor A2a/0.450
1ezfIN0Squalene synthase2.5.1.210.449
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.449
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.449
2bunFADAppA protein/0.449
2ix5FADAcyl-coenzyme A oxidase 4, peroxisomal1.3.3.60.449
2vcmM11Isopenicillin N synthase1.21.3.10.449
3nugNADPyridoxal 4-dehydrogenase1.1.1.1070.449
3nx4NAPPutative oxidoreductase/0.449
3umvFADDeoxyribodipyrimidine photo-lyase4.1.99.30.449
3vt3VDXVitamin D3 receptor/0.449
3w32W32Epidermal growth factor receptor2.7.10.10.449
3w5p4OAVitamin D3 receptor/0.449
4hxyNDPPlm1/0.449
4l8u9AZSerum albumin/0.449
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.448
1ie9VDXVitamin D3 receptor/0.448
1uydPU8Heat shock protein HSP 90-alpha/0.448
2hu2NADC-terminal binding protein 1/0.448
3g49NAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.448
3mnrSD1Heat shock protein HSP 90-alpha/0.448
3n7uNADFormate dehydrogenase, chloroplastic/mitochondrial/0.448
3poz03PEpidermal growth factor receptor2.7.10.10.448
3u4cNDPNADPH-dependent reductase BacG/0.448
3vt8YI3Vitamin D3 receptor/0.448
3vthAPCCarbamoyltransferase/0.448
3w0gW07Vitamin D3 receptor/0.448
4ekkANPRAC-alpha serine/threonine-protein kinase2.7.11.10.448
4h50NAPBiphenyl dioxygenase ferredoxin reductase subunit/0.448
4ia7BIVVitamin D3 receptor A/0.448
4xldBRLPeroxisome proliferator-activated receptor gamma/0.448
5eccNAPDehydrofolate reductase type I/0.448
5k2cZMAAdenosine receptor A2a/0.448
1bw9NADPhenylalanine dehydrogenase/0.447
1d3hA26Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.447
2bd0NAPSepiapterin reductase/0.447
2f4bEHAPeroxisome proliferator-activated receptor gamma/0.447
2iw84SPCyclin-dependent kinase 22.7.11.220.447
2q61SF1Peroxisome proliferator-activated receptor gamma/0.447
2q6sPLBPeroxisome proliferator-activated receptor gamma/0.447
2zlcVDXVitamin D3 receptor/0.447
3vrtYS2Vitamin D3 receptor/0.447
3w0aDS5Vitamin D3 receptor/0.447
4djaFAD(6-4) photolyase/0.447
4g1d0VKVitamin D3 receptor A/0.447
4g1z0VPVitamin D3 receptor A/0.447
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.447
4hfmNAP2-alkenal reductase (NADP(+)-dependent)/0.447
4y95746Tyrosine-protein kinase/0.447
5jtbZMAAdenosine receptor A2a/0.447
1gufNDPEnoyl-[acyl-carrier-protein] reductase 1, mitochondrial1.3.1.100.446
1ie4T44Transthyretin/0.446
1menGARTrifunctional purine biosynthetic protein adenosine-32.1.2.20.446
1uyfPU1Heat shock protein HSP 90-alpha/0.446
2c12FADNitroalkane oxidase1.7.3.10.446
2dcnADP2-keto-3-deoxy-gluconate kinase/0.446
2jn3JN3Fatty acid-binding protein, liver/0.446
2qo9ANPEphrin type-A receptor 32.7.10.10.446
3d7kD7KBenzaldehyde lyase/0.446
3jqpA2PFerredoxin--NADP reductase, apicoplast/0.446
3unk0BYCyclin-dependent kinase 22.7.11.220.446
3w0yDS4Vitamin D3 receptor/0.446
4cd2FOLDihydrofolate reductase1.5.1.30.446
4ia1BIVVitamin D3 receptor A/0.446
4iteTEYVitamin D3 receptor/0.446
4jl5ADPAdenylate kinase/0.446
4qms1N1Serine/threonine-protein kinase 242.7.11.10.446
1ot7CHCBile acid receptor/0.445
1uyePU9Heat shock protein HSP 90-alpha/0.445
2h55DZ8Heat shock protein HSP 90-alpha/0.445
3b6zCO7Enoyl reductase LovC10.445
3ijdC2FMethylenetetrahydrofolate reductase/0.445
3m7rVDXVitamin D3 receptor/0.445
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.445
4jvf17XRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.445
4njoNADD-3-phosphoglycerate dehydrogenase, putative/0.445
5iqeGNPBifunctional AAC/APH2.3.10.445
1oi9N20Cyclin-dependent kinase 22.7.11.220.444
1p8dCO1Oxysterols receptor LXR-beta/0.444
1q1wFADPutidaredoxin reductase1.18.1.50.444
1y4lSVRBasic phospholipase A2 homolog 2/0.444
1zgyBRLPeroxisome proliferator-activated receptor gamma/0.444
2jb4A14Isopenicillin N synthase1.21.3.10.444
2obyNAPQuinone oxidoreductase PIG310.444
2q5p241Peroxisome proliferator-activated receptor gamma/0.444
2wotZZGTGF-beta receptor type-12.7.11.300.444
2x0iNAIMalate dehydrogenase/0.444
3gbuATPUncharacterized sugar kinase PH14592.7.10.444
3ibdCPZCytochrome P450 2B61.14.130.444
3qwbNDPProbable quinone oxidoreductase1.6.5.50.444
3r04UNQSerine/threonine-protein kinase pim-12.7.11.10.444
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
4l9kEHFSerum albumin/0.444
5a3cNADSIR2 family protein/0.444
5iua6DXAdenosine receptor A2a/0.444
3emlZMAAdenosine receptor A2a/0.444
1fmlRTLRetinol dehydratase/0.443
1qiqACCIsopenicillin N synthase1.21.3.10.443
2hcdBIVVitamin D3 receptor A/0.443
2om9AJAPeroxisome proliferator-activated receptor gamma/0.443
2qocANPEphrin type-A receptor 32.7.10.10.443
3h65I2C5,10-methenyltetrahydromethanopterin hydrogenase1.12.98.20.443
3tdl11DSerum albumin/0.443
3vt45YIVitamin D3 receptor/0.443
3w5rLOAVitamin D3 receptor/0.443
4b99R4LMitogen-activated protein kinase 72.7.11.240.443
4h4uNDPBiphenyl dioxygenase ferredoxin reductase subunit/0.443
4qi5FADCellobiose dehydrogenase/0.443
1e3eNAIAlcohol dehydrogenase 41.1.1.10.442
1g6cTZPThiamine-phosphate synthase/0.442
1np7FADCryptochrome DASH/0.442
1s0zEB1Vitamin D3 receptor/0.442
2eixFADNADH-cytochrome b5 reductase/0.442
2g76NADD-3-phosphoglycerate dehydrogenase1.1.1.950.442
2j8zNAPQuinone oxidoreductase PIG310.442
2ktdPUCProstaglandin-H2 D-isomerase5.3.99.20.442
3iw5DF3Mitogen-activated protein kinase 14/0.442
3wmxNADNAD dependent epimerase/dehydratase/0.442
4bcrWY1Peroxisome proliferator-activated receptor alpha/0.442
4eiyZMAAdenosine receptor A2a/0.442
4g2i0VQVitamin D3 receptor/0.442
4gk4L90Ephrin type-A receptor 32.7.10.10.442
4hjfC2EGGDEF family protein/0.442
4l9q9TPSerum albumin/0.442
4mxxDB8Proto-oncogene tyrosine-protein kinase Src2.7.10.20.442
4nmdFDABifunctional protein PutA/0.442
1db1VDXVitamin D3 receptor/0.441
1mb9ATPCarboxyethyl-arginine beta-lactam-synthase6.3.3.40.441
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.441
1qvrANPChaperone protein ClpB/0.441
2fhnBNIAvidin-related protein 4/5/0.441
2hb7O1CVitamin D3 receptor/0.441
2pmdGNPTranslation initiation factor 2 subunit gamma/0.441
2x19GTPGTP-binding nuclear protein GSP1/CNR1/0.441
3k5hATPPhosphoribosyl-aminoimidazole carboxylase/0.441
3ma301ISerine/threonine-protein kinase pim-12.7.11.10.441
3rmf20ZCyclin-dependent kinase 22.7.11.220.441
3sz0FADSulfide-quinone reductase/0.441
4tuvCPZCytochrome P450 1191.140.441
4tvbNADHomospermidine synthase2.5.1.440.441
5bylGCPBifunctional AAC/APH2.3.10.441
1c2tGARPhosphoribosylglycinamide formyltransferase/0.440
1levCLIFructose-1,6-bisphosphatase 13.1.3.110.440
1pzfA3DLactate dehydrogenase/0.440
1r2jFADFkbI/0.440
1s19MC9Vitamin D3 receptor/0.440
2bgjFADNADPH:ferredoxin reductase/0.440
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.440
2znnS44Peroxisome proliferator-activated receptor alpha/0.440
3d5fL41Peroxisome proliferator-activated receptor delta/0.440
3dr1C5DVitamin D3 receptor A/0.440
3owaFADAcyl-CoA dehydrogenase/0.440
3qrwNDPPutative ketoacyl reductase1.3.10.440
3tvuB37Acetyl-CoA carboxylase/0.440
3vrvYSDVitamin D3 receptor/0.440
4aicNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.440
4ambDUDPutative glycosyl transferase/0.440
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.440
4jlj1NMDeoxycytidine kinase2.7.1.740.440
4nxuADPMitochondrial dynamics protein MID51/0.440
5adhAPRAlcohol dehydrogenase E chain1.1.1.10.440
5br4NADLactaldehyde reductase1.1.1.770.440
5k2dZMAAdenosine receptor A2a/0.440