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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
2mokFMNFlavodoxin 1

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2mokFMNFlavodoxin 1/1.000
4n82FMNRibonucleotide reductase (NrdI family protein), putative/0.509
3bi6396Wee1-like protein kinase2.7.10.20.499
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.499
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.498
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.490
2fcrFMNFlavodoxin/0.487
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.486
4bfxZVXPantothenate kinase2.7.1.330.485
1cznFMNFlavodoxin/0.484
3f90FMNFlavodoxin/0.484
3hxdBD7Geranylgeranyl transferase type-2 subunit beta2.5.1.600.484
2v5uFMNFlavodoxin/0.482
3pz3PZ3Geranylgeranyl transferase type-2 subunit beta2.5.1.600.477
4c2z646Glycylpeptide N-tetradecanoyltransferase 1/0.477
4x7zZM3Mycinamicin III 3''-O-methyltransferase2.1.1.2370.477
3hxfBD9Geranylgeranyl transferase type-2 subunit beta2.5.1.600.475
1z71L17Prothrombin3.4.21.50.474
2wsa646Glycylpeptide N-tetradecanoyltransferase/0.474
3kozZ97D-ornithine 4,5-aminomutase subunit beta/0.474
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.474
1ahnFMNFlavodoxin 1/0.473
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.473
2a2dANPN-acetylgalactosamine kinase2.7.1.1570.472
2cleF6FTryptophan synthase alpha chain/0.472
3qe2FMNNADPH--cytochrome P450 reductase/0.471
4ambDUDPutative glycosyl transferase/0.470
3irhDTPHD domain protein/0.469
4gts7TPGeranylgeranyl transferase type-2 subunit beta2.5.1.600.469
1re0AFBADP-ribosylation factor 1/0.468
1re0AFBARF guanine-nucleotide exchange factor 1/0.468
4a2zVIQGlycylpeptide N-tetradecanoyltransferase/0.468
1fmjRTLRetinol dehydratase/0.467
1fx1FMNFlavodoxin/0.467
1oc1ASVIsopenicillin N synthase1.21.3.10.467
1tilATPAnti-sigma F factor/0.467
2vn1FK5Peptidylprolyl isomerase/0.467
1j9gFMNFlavodoxin/0.466
3zc3FADFerredoxin--NADP reductase1.18.1.20.466
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.466
4y7cFMNNADPH--cytochrome P450 reductase/0.466
2geuCOKPantothenate kinase2.7.1.330.465
4x81MVIMycinamicin III 3''-O-methyltransferase2.1.1.2370.465
1akwFMNFlavodoxin/0.464
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.464
2ejzSAHDiphthine synthase/0.463
2wowNDPTrypanothione reductase/0.463
2y6fM9FIsopenicillin N synthase1.21.3.10.463
3c72CX1Geranylgeranyl transferase type-2 subunit beta2.5.1.600.463
3hxcBD6Geranylgeranyl transferase type-2 subunit beta2.5.1.600.462
4b4vL34Bifunctional protein FolD/0.462
1nm6L86Prothrombin3.4.21.50.461
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.461
2o1xTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.461
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.461
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.461
1fvpFMANon-fluorescent flavoprotein/0.460
3l0lHC3Nuclear receptor ROR-gamma/0.460
4b4w9L9Bifunctional protein FolD/0.460
1j9zFADNADPH--cytochrome P450 reductase/0.459
4bfsZVSPantothenate kinase2.7.1.330.459
4rh10TTSpore photoproduct lyase/0.459
2a94AP0L-lactate dehydrogenase1.1.1.270.458
2fznFADBifunctional protein PutA1.5.5.20.458
3ad9NADSubunit alpha of sarocosine oxidase/0.458
3uovFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.458
4af6FADFerredoxin--NADP reductase, leaf isozyme, chloroplastic1.18.1.20.458
4bb3KKAIsopenicillin N synthase1.21.3.10.458
5fd8A5APutative carboxypeptidase yocD/0.458
1j8qFMNFlavodoxin/0.457
3f6rFMNFlavodoxin/0.457
3qfrFMNNADPH--cytochrome P450 reductase/0.457
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.457
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.457
1trgCB3Thymidylate synthase/0.456
1zklIBMHigh affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A3.1.4.530.456
2zb8IMNProstaglandin reductase 21.3.1.480.456
1fmlRTLRetinol dehydratase/0.455
1obnASVIsopenicillin N synthase1.21.3.10.455
1r8qAFBCytohesin-2/0.455
1r8qAFBADP-ribosylation factor 1/0.455
1udtVIAcGMP-specific 3',5'-cyclic phosphodiesterase/0.455
3br3ETHTH-type transcriptional regulator QacR/0.455
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.455
3zhsTD6Multifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.455
5kf9ACOPredicted acetyltransferase/0.455
1mvsDTMDihydrofolate reductase1.5.1.30.454
2in6839Wee1-like protein kinase2.7.10.20.454
2pncCLUPrimary amine oxidase, liver isozyme/0.454
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.454
5fm7ADPRuvB-like helicase/0.454
1nceCB3Thymidylate synthase/0.453
1tllFADNitric oxide synthase, brain1.14.13.390.453
2cibCM6Lanosterol 14-alpha demethylase1.14.13.700.452
2xlrFADPutative flavin-containing monooxygenase/0.452
3mhpFADFerredoxin--NADP reductase, leaf isozyme, chloroplastic1.18.1.20.452
3rl45GPMetallophosphoesterase MPPED23.10.452
3zkuHCVIsopenicillin N synthase1.21.3.10.452
4fhf0TTSpore photoproduct lyase/0.452
4l9q9TPSerum albumin/0.452
2uuk897Prothrombin3.4.21.50.451
3zoiM2WIsopenicillin N synthase1.21.3.10.451
4bftZVTPantothenate kinase2.7.1.330.451
1azlFMNFlavodoxin/0.450
1lwiNAP3-alpha-hydroxysteroid dehydrogenase1.1.1.500.450
1oytFSNProthrombin3.4.21.50.450
1s3uTQDDihydrofolate reductase1.5.1.30.450
1uhoVDNcGMP-specific 3',5'-cyclic phosphodiesterase/0.450
2e94364Geranylgeranyl pyrophosphate synthase/0.450
2fb8215Serine/threonine-protein kinase B-raf2.7.11.10.450
2wjoQUDBeta-secretase 13.4.23.460.450
2zu9GDPMannosyl-3-phosphoglycerate synthase2.4.1.2170.450
3h3sH15Collagen type IV alpha-3-binding protein/0.450
3kapFMNFlavodoxin/0.450
4e0hFADMitochondrial FAD-linked sulfhydryl oxidase ERV11.8.3.20.450
4rxsTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.450
1eq2ADQADP-L-glycero-D-manno-heptose-6-epimerase/0.449
1mu6CDAProthrombin3.4.21.50.449
1so2666cGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.449
2ewmNAD(S)-1-Phenylethanol dehydrogenase1.1.1.3110.449
3adaNADSubunit alpha of sarocosine oxidase/0.449
3fpkFADFerredoxin-NADP reductase/0.449
3qfcFADNADPH--cytochrome P450 reductase/0.449
4b5oACOAlpha-tubulin N-acetyltransferase 1/0.449
4bfvZVVPantothenate kinase2.7.1.330.449
4d9eLCSD-cysteine desulfhydrase/0.449
4e2xTYDMethyltransferase/0.449
4rvgTYDD-mycarose 3-C-methyltransferase/0.449
5dp2NAPCurF/0.449
5fx2FMNFlavodoxin/0.449
1ycfFMNNitric oxide reductase10.448
2d3aADPGlutamine synthetase root isozyme 36.3.1.20.448
2g8yNADHydroxycarboxylate dehydrogenase B/0.448
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.448
2pnjCHDFerrochelatase, mitochondrial4.99.1.10.448
3bgxMEFThymidylate synthase/0.448
3gwfFADCyclohexanone monooxygenase/0.448
3i0pNADMalate dehydrogenase, putative/0.448
3koyZ97D-ornithine 4,5-aminomutase subunit beta/0.448
3uyk0CXProbable NDP-rhamnosyltransferase/0.448
4bfwZVWPantothenate kinase2.7.1.330.448
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.448
3sn6P0GBeta-2 adrenergic receptor/0.448
1amoFMNNADPH--cytochrome P450 reductase/0.447
1f4fTP3Thymidylate synthase/0.447
1x1bSAHC-20 methyltransferase/0.447
1zgyBRLPeroxisome proliferator-activated receptor gamma/0.447
1zknIBMcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.447
2ij7TPFMycocyclosin synthase1.14.21.90.447
2pswCOAN-alpha-acetyltransferase 50/0.447
2znpK55Peroxisome proliferator-activated receptor delta/0.447
3udk095Beta-secretase 13.4.23.460.447
4g95OAGDihydrofolate reductase1.5.1.30.447
1itzTPPTransketolase, chloroplastic2.2.1.10.446
1knpFADL-aspartate oxidase1.4.3.160.446
2wo7ASVIsopenicillin N synthase1.21.3.10.446
4a83DXCMajor pollen allergen Bet v 1-A/0.446
4fqsLYAThymidylate synthase ThyA/0.446
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.446
4qofFMNRibosyldihydronicotinamide dehydrogenase [quinone]/0.446
1f4gTP4Thymidylate synthase/0.445
1gjrFADFerredoxin--NADP reductase1.18.1.20.445
2bdyUNBProthrombin3.4.21.50.445
2xytTC9Soluble acetylcholine receptor/0.445
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
3hu3AGSTransitional endoplasmic reticulum ATPase3.6.4.60.445
3lkhLT6Genome polyprotein2.7.7.480.445
3o56ZG1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.445
3pqbVGPPutative oxidoreductase/0.445
3slkNDPPolyketide synthase extender module 2/0.445
3to3ATPPetrobactin biosynthesis protein AsbB/0.445
3ufl508Beta-secretase 13.4.23.460.445
3w2fNADNADH-cytochrome b5 reductase 31.6.2.20.445
4g3jVNTLanosterol 14-alpha-demethylase/0.445
4gi40EXQueuine tRNA-ribosyltransferase2.4.2.290.445
4uajFADNa(+)-translocating NADH-quinone reductase subunit F/0.445
1cbfSAHCobalt-precorrin-4 C(11)-methyltransferase2.1.1.2710.444
1crbRTLRetinol-binding protein 1/0.444
1jqdSAHHistamine N-methyltransferase2.1.1.80.444
1jtqLY3Thymidylate synthase/0.444
1kceCB3Thymidylate synthase/0.444
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.444
1yqxNAPSinapyl alcohol dehydrogenase/0.444
2a4nCOAAac(6')-Ii protein/0.444
2e0nSAHPrecorrin-2 C20-methyltransferase/0.444
2o7oDXTTetracycline repressor protein class D/0.444
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.444
3f3y4OABile salt sulfotransferase2.8.2.140.444
3hl0NADMaleylacetate reductase/0.444
3hv3R49Mitogen-activated protein kinase 14/0.444
3o4rNAPDehydrogenase/reductase SDR family member 41.1.1.1840.444
4fx2FMNFlavodoxin/0.444
4jtqNAPAldo-keto reductase family 1 member C2/0.444
4tnzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.444
1kzjCB3Thymidylate synthase/0.443
1nzq162Prothrombin3.4.21.50.443
2c94TSF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.443
2clfF6FTryptophan synthase alpha chain/0.443
2d4vNADIsocitrate dehydrogenase [NADP]/0.443
2jh6894Prothrombin3.4.21.50.443
3ggcH26Hypoxanthine-guanine phosphoribosyltransferase2.4.2.80.443
3hxbBD5Geranylgeranyl transferase type-2 subunit beta2.5.1.600.443
3tfuPL8Adenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.443
1d3dBZTProthrombin3.4.21.50.442
1kw6BPYBiphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.442
1uaeUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.442
2vqoTFGHistone deacetylase 43.5.1.980.442
3dv0TPWPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.442
3dv0TPWPyruvate dehydrogenase E1 component subunit beta1.2.4.10.442
3ojxFADNADPH--cytochrome P450 reductase/0.442
3pe2E1BCasein kinase II subunit alpha2.7.11.10.442
3rtnRTNBeta-secretase 13.4.23.460.442
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.442
3uptTPPTransketolase/0.442
5kgjACOPredicted acetyltransferase/0.442
1g7uPEP2-dehydro-3-deoxyphosphooctonate aldolase2.5.1.550.441
1x8b824Wee1-like protein kinase2.7.10.20.441
2bn4FMNNADPH--cytochrome P450 reductase/0.441
2vkeTACTetracycline repressor protein class D/0.441
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
4gevCB3Thymidylate synthase/0.441
1m9nAMZBifunctional purine biosynthesis protein PURH2.1.2.30.440
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
1tysDHFThymidylate synthase/0.440
1w19T5P6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.440
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
2idkC2FGlycine N-methyltransferase2.1.1.200.440
2ipiAKYAclacinomycin-N/aclacinomycin-A oxidase/0.440
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.440
3s5wFADL-ornithine N(5)-monooxygenase/0.440
3sp9IL2Peroxisome proliferator-activated receptor delta/0.440
3udn09BBeta-secretase 13.4.23.460.440
3zhvTDWMultifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.440
4irnFADAnaB/0.440
4xo7NAPAldo-keto reductase family 1 member C2/0.440