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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities 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

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
1fndA2PFerredoxin--NADP reductase, chloroplastic1.18.1.2

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
1fndA2PFerredoxin--NADP reductase, chloroplastic1.18.1.21.000
2rc6NAPFerredoxin--NADP reductase/0.560
2p9gNAID-3-phosphoglycerate dehydrogenase1.1.1.950.485
5iqhGNPBifunctional AAC/APH2.3.10.484
4ia3BIVVitamin D3 receptor A/0.482
2bpoNAPNADPH--cytochrome P450 reductase/0.479
4b5pACOAlpha-tubulin N-acetyltransferase 1/0.479
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.478
4y9rNAPNADPH--cytochrome P450 reductase/0.478
1lhwESMSex hormone-binding globulin/0.477
2hcdBIVVitamin D3 receptor A/0.476
1q4u4CA4-hydroxybenzoyl-CoA thioesterase3.1.2.230.473
2rhrEMOPutative ketoacyl reductase1.3.10.473
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.473
4ruoBIVVitamin D3 receptor A/0.472
1dkfBMSRetinoic acid receptor alpha/0.470
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.469
2bf4NAPNADPH--cytochrome P450 reductase/0.468
2ay3MPPAromatic-amino-acid aminotransferase2.6.1.570.467
3ptzUDXUDP-glucose 6-dehydrogenase1.1.1.220.467
1orkATCTetracycline repressor protein class D/0.464
4iah1DXAlr2278 protein/0.464
3qlrNDPDihydrofolate reductase1.5.1.30.463
4k5p1OSM1 family aminopeptidase3.4.110.463
3uleC69Actin-related protein 3/0.462
3nr4PYVAbscisic acid receptor PYL2/0.461
4i3vNADAldehyde dehydrogenase (NAD+)/0.461
1p0pBCHCholinesterase3.1.1.80.460
2i4jDRJPeroxisome proliferator-activated receptor gamma/0.460
2prh238Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.460
2xb5I7TTetracycline repressor protein class D/0.460
2y1oT26UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.459
3elm24FCollagenase 33.4.240.459
4ia7BIVVitamin D3 receptor A/0.459
1m4dCOAAminoglycoside 2'-N-acetyltransferase2.3.10.458
1osvCHCBile acid receptor/0.458
2ejvNADL-threonine 3-dehydrogenase/0.458
3nmpPYVAbscisic acid receptor PYL2/0.458
4g95OAGDihydrofolate reductase1.5.1.30.458
1kvtUPGUDP-glucose 4-epimerase5.1.3.20.457
1ppjANYCytochrome b/0.457
2cahNDPCatalase1.11.1.60.457
3vt8YI3Vitamin D3 receptor/0.457
1g6cIFPThiamine-phosphate synthase/0.456
1v9aSAHUncharacterized protein/0.456
2i0zFADNAD(FAD)-utilizing dehydrogenases/0.456
3ijdC2FMethylenetetrahydrofolate reductase/0.456
3r34COA4-hydroxybenzoyl-CoA thioesterase3.1.2.230.456
1hpuA12Protein UshA3.1.3.50.455
1j39UPGDNA beta-glucosyltransferase/0.455
3iqeH4MF420-dependent methylenetetrahydromethanopterin dehydrogenase1.5.98.10.455
3jynNDPQuinone oxidoreductase/0.455
3s79ASDAromatase1.14.14.140.455
4yau2AMNADPH--cytochrome P450 reductase/0.455
5cb3APRO-acetyl-ADP-ribose deacetylase/0.455
1lriCLRBeta-elicitin cryptogein/0.454
2yfeYFEPeroxisome proliferator-activated receptor gamma/0.454
4dc0NDPPutative ketoacyl reductase1.3.10.454
4emyPLPAminotransferase class I and II/0.454
4s26SAHPhosphomethylpyrimidine synthase, chloroplastic4.1.99.170.454
5koiNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.454
1chwHXCChalcone synthase 22.3.1.740.453
1uxnNAPNAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenase/0.453
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.453
2fypRDEEndoplasmin/0.453
2ktdPUCProstaglandin-H2 D-isomerase5.3.99.20.453
2oapANPType II secretion system protein (GspE-2)/0.453
2om9AJAPeroxisome proliferator-activated receptor gamma/0.453
2r0cFADPutative FAD-monooxygenase/0.453
3ez2ADPPlasmid partition protein A/0.453
3r354CO4-hydroxybenzoyl-CoA thioesterase3.1.2.230.453
3tea4CO4-hydroxybenzoyl-CoA thioesterase3.1.2.230.453
1dxoFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.452
1equEQIEstradiol 17-beta-dehydrogenase 11.1.1.620.452
2kceD16Thymidylate synthase/0.452
2y05RALProstaglandin reductase 1/0.452
3f8kCOAUncharacterized protein/0.452
3ix9MTXDihydrofolate reductase1.5.1.30.452
3l6jZ90Alr2278 protein/0.452
4auxXTCTetracycline repressor protein class D/0.452
4ia2BIVVitamin D3 receptor A/0.452
5iqaGNPBifunctional AAC/APH2.3.10.452
3b7dCNIGlutamate receptor 2/0.451
4gt3ATPMitogen-activated protein kinase 12.7.11.240.451
4kxn6K62'-deoxynucleoside 5'-phosphate N-hydrolase 1/0.451
4xgxADPFAD:protein FMN transferase/0.451
5eaiFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.451
1jpaANPEphrin type-B receptor 22.7.10.10.450
1n83CLRNuclear receptor ROR-alpha/0.450
1qaxHMG3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.880.450
1rd4L08Integrin alpha-L/0.450
1t87CAMCamphor 5-monooxygenase1.14.15.10.450
3r3c4CO4-hydroxybenzoyl-CoA thioesterase3.1.2.230.450
4em9TCEPeroxisome proliferator-activated receptor gamma/0.450
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.450
4ia1BIVVitamin D3 receptor A/0.450
4jib1L6cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.450
4wqmFADToluene-4-monooxygenase electron transfer component1.18.1.30.450
4xuhSFIPeroxisome proliferator-activated receptor gamma/0.450
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.449
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.449
1ml6GBXGlutathione S-transferase A22.5.1.180.449
1q4t4CO4-hydroxybenzoyl-CoA thioesterase3.1.2.230.449
1ybmNAPUncharacterized protein At5g02240/0.449
1zzlTZYMitogen-activated protein kinase 14/0.449
2rh9IGPTryptophan synthase alpha chain/0.449
2ylxNAPPhenylacetone monooxygenase1.14.13.920.449
4asyN5YGlucose-1-phosphate thymidylyltransferase/0.449
4g2i0VQVitamin D3 receptor/0.449
4j03FVSBifunctional epoxide hydrolase 23.1.3.760.449
4qknJMSAlpha-ketoglutarate-dependent dioxygenase FTO/0.449
1dr3HBIDihydrofolate reductase1.5.1.30.448
1ie8KH1Vitamin D3 receptor/0.448
1uu3LY43-phosphoinositide-dependent protein kinase 12.7.11.10.448
2xgoZKDUncharacterized protein/0.448
2zbaZBATrichothecene 3-O-acetyltransferase/0.448
3tm5SFGUncharacterized protein/0.448
4bzo676Serine/threonine-protein kinase pim-12.7.11.10.448
4ceqQCHIntegrase/0.448
4g3pUD1Bifunctional protein GlmU/0.448
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
4l3l5FIRibosomal protein S6 kinase beta-12.7.11.10.448
4l4xNDPAmphI/0.448
4qe6JN3Bile acid receptor/0.448
5ajqDB8Serine/threonine-protein kinase 102.7.11.10.448
1d3gBREDihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.447
1fpqSAMIsoliquiritigenin 2'-O-methyltransferase/0.447
2trtTACTetracycline repressor protein class D/0.447
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3fxuTSUHTH-type transcriptional regulator TsaR/0.447
3ml8ML8Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.447
3r374CO4-hydroxybenzoyl-CoA thioesterase3.1.2.230.447
3tqhNDPQuinone oxidoreductase/0.447
4bznUGXSerine/threonine-protein kinase pim-12.7.11.10.447
4ezl0SEPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.447
4fhh0U3Vitamin D3 receptor A/0.447
4nmdFDABifunctional protein PutA/0.447
1d3hA26Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.446
1ewyFADFerredoxin--NADP reductase1.18.1.20.446
1g4tFTPThiamine-phosphate synthase/0.446
1r6g442Thyroid hormone receptor beta/0.446
1y4lSVRBasic phospholipase A2 homolog 2/0.446
2fzhDH1Dihydrofolate reductase1.5.1.30.446
2vwqNAPGlucose 1-dehydrogenase/0.446
4ez8DHFThymidylate synthase2.1.1.450.446
4ho8THMGlucose-1-phosphate thymidylyltransferase/0.446
4mlhVO2Glucokinase2.7.1.20.446
4zm3PLPAminotransferase/0.446
1bwkFMNNADPH dehydrogenase 11.6.99.10.445
1xonPILcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.445
2ay84TBAromatic-amino-acid aminotransferase2.6.1.570.445
2zb45OPProstaglandin reductase 21.3.1.480.445
2zbzVDXVitamin D3 dihydroxylase/0.445
3fnhJPJEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.445
3nugNADPyridoxal 4-dehydrogenase1.1.1.1070.445
3up0D7SaceDAF-12/0.445
3wmxNADNAD dependent epimerase/dehydratase/0.445
4a4wYFBPeroxisome proliferator-activated receptor gamma/0.445
4a7cE46Serine/threonine-protein kinase pim-12.7.11.10.445
4c77N01Phenylacetone monooxygenase1.14.13.920.445
4q71FADBifunctional protein PutA/0.445
4zcaADPKinesin-like protein KIF11/0.445
1tduCB3Thymidylate synthase/0.444
1trgCB3Thymidylate synthase/0.444
1yqj6NPMitogen-activated protein kinase 14/0.444
2obyNAPQuinone oxidoreductase PIG310.444
2q6sPLBPeroxisome proliferator-activated receptor gamma/0.444
2ydoADNAdenosine receptor A2a/0.444
3vt7VDXVitamin D3 receptor/0.444
3zu2NAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.444
4eu4COASuccinyl-CoA:acetate CoA-transferase/0.444
4jvb1M0Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.444
5bylGCPBifunctional AAC/APH2.3.10.444
1gjrNAPFerredoxin--NADP reductase1.18.1.20.443
1i2bNADUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.443
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.443
1kceCB3Thymidylate synthase/0.443
1pl8NADSorbitol dehydrogenase1.1.1.140.443
1s0xC3SNuclear receptor ROR-alpha/0.443
1suiFRECaffeoyl-CoA O-methyltransferase2.1.1.1040.443
2i4pDRHPeroxisome proliferator-activated receptor gamma/0.443
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.443
3ictADPCoenzyme A disulfide reductase/0.443
3oafOAGDihydrofolate reductase1.5.1.30.443
3okxSAMS-adenosyl-L-methionine-binding protein RPA0152/0.443
3t2zFADSulfide-quinone reductase/0.443
4c717RD3-oxoacyl-ACP synthase/0.443
4f1yCNIGlutamate receptor 3/0.443
4g1z0VPVitamin D3 receptor A/0.443
4zbrNPSSerum albumin/0.443
1njfAGSDNA polymerase III subunit tau2.7.7.70.442
1rx8NAPDihydrofolate reductase1.5.1.30.442
2ftoCB3Thymidylate synthase/0.442
2gcgNDPGlyoxylate reductase/hydroxypyruvate reductase1.1.1.790.442
2xpvMIYTetracycline repressor protein class D/0.442
2y30SM8Putative repressor SimReg2/0.442
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3adaNADSubunit alpha of sarocosine oxidase/0.442
3koo24DBifunctional epoxide hydrolase 23.3.2.100.442
3r3d4CO4-hydroxybenzoyl-CoA thioesterase3.1.2.230.442
4e37NDPCatalase1.11.1.60.442
4nky3QZSteroid 17-alpha-hydroxylase/17,20 lyase/0.442
4q73FADBifunctional protein PutA/0.442
4tuvCPZCytochrome P450 1191.140.442
5cwa0GAAnthranilate synthase component 14.1.3.270.442
5ifyUMPGlucose-1-phosphate thymidylyltransferase/0.442
1a8t061Metallo-beta-lactamase type 2/0.441
1dxyNADD-2-hydroxyisocaproate dehydrogenase1.1.10.441
1g0nNDPTetrahydroxynaphthalene reductase1.1.1.2520.441
1mjhATPUniversal stress protein MJ0577/0.441
1piwNAPNADP-dependent alcohol dehydrogenase 61.1.1.20.441
1y2d4DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.441
1zidZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.441
2azyCHDPhospholipase A2, major isoenzyme3.1.1.40.441
2hayFMNPutative NAD(P)H-flavin oxidoreductase/0.441
2iebZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.441
2iluNDPLactaldehyde dehydrogenase1.2.1.220.441
2ivpATPtRNA N6-adenosine threonylcarbamoyltransferase/0.441
3bejMUFBile acid receptor/0.441
3etdNDPGlutamate dehydrogenase 1, mitochondrial1.4.1.30.441
3irm1CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.441
3k145352-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase/0.441
3nj0PYVAbscisic acid receptor PYL2/0.441
3vt45YIVitamin D3 receptor/0.441
3w0jT08Vitamin D3 receptor/0.441
4g2fC07Ephrin type-A receptor 32.7.10.10.441
4hl1ZZ7Metallo-beta-lactamase type 2/0.441
4jqh1MFAlr2278 protein/0.441
4mihFADPyranose 2-oxidase1.1.3.100.441
4rujVDXVitamin D3 receptor A/0.441
4zrnUPGUDP-glucose 4-epimerase, putative/0.441
1kzjCB3Thymidylate synthase/0.440
1likADNAdenosine kinase2.7.1.200.440
1m75CAAHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.440
1nq7ARLNuclear receptor ROR-beta/0.440
1nzfUPGDNA beta-glucosyltransferase/0.440
1pn3TYDdTDP-epi-vancosaminyltransferase2.4.1.3110.440
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.440
1s0zEB1Vitamin D3 receptor/0.440
1s3zCOAAminoglycoside N(6')-acetyltransferase type 1/0.440
1uuoBRFDihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.440
1x7gNAPPutative ketoacyl reductase1.3.10.440
2ch6ADPN-acetyl-D-glucosamine kinase2.7.1.590.440
2gmvPEPPhosphoenolpyruvate carboxykinase, cytosolic [GTP]4.1.1.320.440
2hbhXE4Vitamin D3 receptor A/0.440
2hc4VDXVitamin D3 receptor A/0.440
2ic5GDPRas-related C3 botulinum toxin substrate 3/0.440
2j2iLY4Serine/threonine-protein kinase pim-12.7.11.10.440
3cy2MB9Serine/threonine-protein kinase pim-12.7.11.10.440
3hkoANPCalcium/calmodulin-dependent protein kinase with a kinase domain and 2 calmodulin-like EF hands/0.440
3pqbVGPPutative oxidoreductase/0.440
3r324CO4-hydroxybenzoyl-CoA thioesterase3.1.2.230.440
4j49NAIUncharacterized protein/0.440
4nb6444Nuclear receptor ROR-gamma/0.440
4z64ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.440
5dozNDPJamJ/0.440
5iqbGNPBifunctional AAC/APH2.3.10.440
5k2aZMAAdenosine receptor A2a/0.440