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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
2wmdZZ0NmrA-like family domain-containing protein 1

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
2wmdZZ0NmrA-like family domain-containing protein 1/1.000
2wm3NFLNmrA-like family domain-containing protein 1/0.537
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.506
4emdC5P4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.503
1r2jFADFkbI/0.498
4u140HKMuscarinic acetylcholine receptor M3/0.493
1ay0TPPTransketolase 12.2.1.10.489
2xlrFADPutative flavin-containing monooxygenase/0.488
4a322CDGlycylpeptide N-tetradecanoyltransferase/0.487
2qimZEAClass 10 plant pathogenesis-related protein/0.483
1c7oPPGHemolysin/0.482
2wsa646Glycylpeptide N-tetradecanoyltransferase/0.482
2whqHI6Acetylcholinesterase3.1.1.70.481
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.481
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.480
3pqbVGPPutative oxidoreductase/0.480
3uzxAOM3-oxo-5-beta-steroid 4-dehydrogenase/0.479
4jt91NSNAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.10.479
2g8yNADHydroxycarboxylate dehydrogenase B/0.478
2rqfJH3Hemolymph juvenile hormone binding protein/0.478
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.478
3tfuPL8Adenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.475
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.474
2xveFADPutative flavin-containing monooxygenase/0.473
3qftFADNADPH--cytochrome P450 reductase/0.473
3uzxAOX3-oxo-5-beta-steroid 4-dehydrogenase/0.473
2g1r3IGRenin3.4.23.150.472
3gwfNAPCyclohexanone monooxygenase/0.472
3af0GDPPantothenate kinase2.7.1.330.469
4dxlC5P4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.469
2c12FADNitroalkane oxidase1.7.3.10.468
2xvfFADPutative flavin-containing monooxygenase/0.468
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.468
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.468
3nubUD0UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.468
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.467
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.467
1w6rGNTAcetylcholinesterase3.1.1.70.466
1sweBTNStreptavidin/0.465
3b9lAZZSerum albumin/0.465
3jsxCC2NAD(P)H dehydrogenase [quinone] 11.6.5.20.465
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.465
3fp0FP015-O-acetyltransferase/0.464
3ozd4CTS-methyl-5'-thioadenosine phosphorylase/0.464
2flhZEACytokinin-specific binding protein/0.463
2g5w8PG12-oxophytodienoate reductase 31.3.1.420.463
2hdjNDPAldo-keto reductase family 1 member C2/0.463
1ni1HFPProtein farnesyltransferase subunit beta2.5.1.580.462
2nmtMIMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.462
3w6hAZMCarbonic anhydrase 14.2.1.10.462
4a2zVIQGlycylpeptide N-tetradecanoyltransferase/0.462
4uugPXGBranched-chain amino acid aminotransferase, putative/0.462
3eksCY9Actin-5C/0.461
3v0p4GWHisto-blood group ABO system transferase/0.461
3zkyWT4Isopenicillin N synthase1.21.3.10.461
1ex75GPGuanylate kinase2.7.4.80.460
1zgbA1EAcetylcholinesterase3.1.1.70.459
3bxxQUEDihydroflavonol 4-reductase1.1.1.2190.459
3kslSZHProtein farnesyltransferase subunit beta2.5.1.580.459
3o4rNAPDehydrogenase/reductase SDR family member 41.1.1.1840.459
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.458
1ry0PG2Aldo-keto reductase family 1 member C3/0.458
2g28TDKPyruvate dehydrogenase E1 component1.2.4.10.458
2gv8NDPThiol-specific monooxygenase1.14.130.458
2vbpVB1Isopenicillin N synthase1.21.3.10.458
2xvhFADPutative flavin-containing monooxygenase/0.458
3uzzTES3-oxo-5-beta-steroid 4-dehydrogenase/0.458
4iilRBFMembrane lipoprotein TpN38(b)/0.458
2bxqIMNSerum albumin/0.457
3uzzASD3-oxo-5-beta-steroid 4-dehydrogenase/0.457
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.457
1x8lOXRRetinol dehydratase/0.456
3lxeTORCarbonic anhydrase 14.2.1.10.456
4bftZVTPantothenate kinase2.7.1.330.456
4bfuZVUPantothenate kinase2.7.1.330.456
4lcw1VYMajor histocompatibility complex class I-related gene protein/0.456
1gky5GPGuanylate kinase2.7.4.80.455
1ygkRRCPyridoxal kinase2.7.1.350.455
3v0m5GWHisto-blood group ABO system transferase/0.455
4bb3KKAIsopenicillin N synthase1.21.3.10.455
4psbGA3Cytokinin-specific binding protein/0.455
4zzi1NSNAD-dependent protein deacetylase sirtuin-13.5.10.455
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.454
1pl6572Sorbitol dehydrogenase1.1.1.140.454
1ve3SAMUncharacterized protein/0.454
2vq7NAPPutative flavin-containing monooxygenase/0.454
3g0cRUFDipeptidyl peptidase 4/0.454
4gdpFADPolyamine oxidase FMS1/0.454
4mlp2CXCryptochrome-2/0.454
1egeFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.453
1eveE20Acetylcholinesterase3.1.1.70.453
1lkeDOGBilin-binding protein/0.453
1swpBTNStreptavidin/0.453
3gf4UPGUDP-galactopyranose mutase5.4.99.90.453
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
3r8hZOMAldo-keto reductase family 1 member C3/0.453
3zkuHCVIsopenicillin N synthase1.21.3.10.453
4jq4IMNAldo-keto reductase family 1 member C2/0.453
4twnB96Ephrin type-A receptor 32.7.10.10.453
1ni12C5Protein farnesyltransferase subunit beta2.5.1.580.452
1nm6L86Prothrombin3.4.21.50.452
3q7fED2Uncharacterized protein/0.452
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.452
4ey6GNTAcetylcholinesterase3.1.1.70.452
1fmlRTLRetinol dehydratase/0.451
1sb1165Prothrombin3.4.21.50.451
1swnBTNStreptavidin/0.451
3eheNADUDP-glucose 4-epimerase (GalE-1)/0.451
3ielU5PRibonuclease TTHA02523.10.451
1lnmDTXBilin-binding protein/0.450
1yw8A75Methionine aminopeptidase 2/0.450
2v58LZJBiotin carboxylase6.3.4.140.450
3fcjFADNitroalkane oxidase1.7.3.10.450
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
5kgjACOPredicted acetyltransferase/0.450
1mepBTNStreptavidin/0.449
1oc1ASVIsopenicillin N synthase1.21.3.10.449
2ejvNADL-threonine 3-dehydrogenase/0.449
4dch4DCGlucokinase2.7.1.20.449
4xmxBESAminopeptidase N3.4.11.20.449
1z8962PAldose reductase1.1.1.210.448
2ea4F79Methionine aminopeptidase 2/0.448
3aosJH2Hemolymph juvenile hormone binding protein/0.448
3gmd2M3Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.448
3u8dU8DPhospholipase A2, membrane associated/0.448
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.448
4dbs0HVAldo-keto reductase family 1 member C3/0.448
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
4oztP1AEcdysone receptor, putative/0.448
4qzuRTLRetinol-binding protein 2/0.448
1mrqSTRAldo-keto reductase family 1 member C1/0.447
1rpwDIDHTH-type transcriptional regulator QacR/0.447
1srfMTBStreptavidin/0.447
1zdwFLVPrenyltransferase/0.447
2g25TDKPyruvate dehydrogenase E1 component1.2.4.10.447
2jb4A14Isopenicillin N synthase1.21.3.10.447
2tctCTCTetracycline repressor protein class D/0.447
3dhcCYKN-acyl homoserine lactonase AiiA3.1.1.810.447
3gwfFADCyclohexanone monooxygenase/0.447
3h3qH13Collagen type IV alpha-3-binding protein/0.447
3zhoFMNNAD(P)H dehydrogenase (quinone)/0.447
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.447
4n3l2FNProthrombin3.4.21.50.447
1enoNADEnoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic1.3.1.90.446
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.446
1o6qR17Squalene--hopene cyclase4.2.1.1290.446
1tilATPAnti-sigma F factor/0.446
1tkaN3TTransketolase 12.2.1.10.446
1w76GNTAcetylcholinesterase3.1.1.70.446
2rtgBTNStreptavidin/0.446
2vbdV10Isopenicillin N synthase1.21.3.10.446
2x1hX1HProstaglandin reductase 310.446
3buvNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.446
3dopNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.446
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
4bfxZVXPantothenate kinase2.7.1.330.446
4r81FMNPredicted NADH dehydrogenase/0.446
1a80NDP2,5-diketo-D-gluconic acid reductase A1.1.1.3460.445
1h22E10Acetylcholinesterase3.1.1.70.445
1odcA8BAcetylcholinesterase3.1.1.70.445
1qtiGNTAcetylcholinesterase3.1.1.70.445
1rfgGMPPurine nucleoside phosphorylase2.4.2.10.445
1thnADPAnti-sigma F factor/0.445
1zg32HIIsoflavone 4'-O-methyltransferase/0.445
2gmsP0PPutative pyridoxamine 5-phosphate-dependent dehydrase/0.445
3cgtBCDCyclomaltodextrin glucanotransferase2.4.1.190.445
3iobA4DPantothenate synthetase6.3.2.10.445
4gh5NADShort-chain dehydrogenase/reductase SDR/0.445
4nv14TGFormyl transferase/0.445
3vw7VPXProteinase-activated receptor 1/0.445
1obnASVIsopenicillin N synthase1.21.3.10.444
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.444
1xzqFONtRNA modification GTPase MnmE3.6.50.444
2a1hGBNBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.444
2jl1NAPTriphenylmethane reductase/0.444
2r2lPB9Protein farnesyltransferase subunit beta2.5.1.580.444
2r8oT5XTransketolase 1/0.444
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3qe2FMNNADPH--cytochrome P450 reductase/0.444
3vgwNVZAvidin/0.444
4b1hAR6Poly(ADP-ribose) glycohydrolase3.2.1.1430.444
4jq3NAPAldo-keto reductase family 1 member C2/0.444
1lczBH7Streptavidin/0.443
1odnAPVIsopenicillin N synthase1.21.3.10.443
2cekN8TAcetylcholinesterase3.1.1.70.443
2iodMYCDihydroflavonol 4-reductase1.1.1.2190.443
2ok8FADFerredoxin--NADP reductase, apicoplast/0.443
3ddw055Glycogen phosphorylase, liver form2.4.1.10.443
3hxdBD7Geranylgeranyl transferase type-2 subunit beta2.5.1.600.443
3prfFP3Serine/threonine-protein kinase B-raf2.7.11.10.443
3q9bB3NAcetylpolyamine amidohydrolase/0.443
3w78CBDFMN-dependent NADH-azoreductase/0.443
3wqmB29Diterpene synthase3.1.7.80.443
4jzr4JREgl nine homolog 1/0.443
5ah5LSSLeucine--tRNA ligase/0.443
1gg5E09NAD(P)H dehydrogenase [quinone] 11.6.5.20.442
1ni4TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.442
1ni4TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.442
1nl4HFPProtein farnesyltransferase subunit beta2.5.1.580.442
1srgMHBStreptavidin/0.442
1v3q2DIPurine nucleoside phosphorylase2.4.2.10.442
2c9bPUG6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.442
3fhxPXLPyridoxal kinase2.7.1.350.442
3fhxPLPPyridoxal kinase2.7.1.350.442
4lngJANCaaX farnesyltransferase beta subunit Ram1/0.442
4m9aFDAAcyl-CoA dehydrogenase/0.442
4rvfTYDD-mycarose 3-C-methyltransferase/0.442
5c1mCLRMu-type opioid receptor/0.442
2ycyP32Beta-1 adrenergic receptor/0.442
1a9zUPGUDP-glucose 4-epimerase5.1.3.20.441
1ut6A8NAcetylcholinesterase3.1.1.70.441
1y2e5DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.441
2pbzATPUncharacterized protein/0.441
2qd3CHDFerrochelatase, mitochondrial4.99.1.10.441
2ywlFADThioredoxin reductase related protein/0.441
3br3ETHTH-type transcriptional regulator QacR/0.441
3cmfPDN3-oxo-5-beta-steroid 4-dehydrogenase/0.441
3ziuLSSLeucyl-tRNA synthetase/0.441
4q0kGA3Phytohormone-binding protein/0.441
4yu153NAldose reductase1.1.1.210.441
5jqhCAUBeta-2 adrenergic receptor/0.441
1q5mNDPProstaglandin-E(2) 9-reductase1.1.1.1890.440
1w4lGL8Acetylcholinesterase3.1.1.70.440
1yhjR6CPyridoxal kinase2.7.1.350.440
2a94AP0L-lactate dehydrogenase1.1.1.270.440
2f3815MAldo-keto reductase family 1 member C3/0.440
2iu8UD1UDP-3-O-acylglucosamine N-acyltransferase2.3.10.440
2p1t3TNRetinoic acid receptor RXR-alpha/0.440
2v59LZKBiotin carboxylase6.3.4.140.440
2vcmM11Isopenicillin N synthase1.21.3.10.440
2xi4AFTAcetylcholinesterase3.1.1.70.440
3g1rNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.440
3gn73GNPoly [ADP-ribose] polymerase 12.4.2.300.440
3hxcBD6Geranylgeranyl transferase type-2 subunit beta2.5.1.600.440
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3zoiM2WIsopenicillin N synthase1.21.3.10.440
4jsr1NQNAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.10.440
4qfxDGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.440
4qfyDCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.440
8catNDPCatalase1.11.1.60.440
5d6lCAUBeta-2 adrenergic receptor/0.440