sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 2ior | ADP | Chaperone protein HtpG |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2ior | ADP | Chaperone protein HtpG | / | 1.000 | |
| 4xcl | AGS | Heat shock cognate 90 kDa protein | / | 0.593 | |
| 3k97 | 4CD | Heat shock protein HSP 90-alpha | / | 0.572 | |
| 4ipe | ANP | TNF receptor-associated protein 1 | / | 0.564 | |
| 3r4o | FU3 | Heat shock protein HSP 90-alpha | / | 0.559 | |
| 4jql | VJ6 | Heat shock protein HSP 90-alpha | / | 0.555 | |
| 4xcj | ADP | Heat shock cognate 90 kDa protein | / | 0.554 | |
| 3wha | WHA | Heat shock protein HSP 90-alpha | / | 0.550 | |
| 2qg0 | A94 | Heat shock protein HSP 90-alpha | / | 0.549 | |
| 2yef | ANP | Heat shock protein HSP 90-alpha | / | 0.548 | |
| 2byh | 2D7 | Heat shock protein HSP 90-alpha | / | 0.544 | |
| 3vha | VHA | Heat shock protein HSP 90-alpha | / | 0.539 | |
| 1osf | KOS | Heat shock protein HSP 90-alpha | / | 0.538 | |
| 2xjj | L81 | Heat shock protein HSP 90-alpha | / | 0.537 | |
| 3hyz | 42C | Heat shock protein HSP 90-alpha | / | 0.537 | |
| 2xab | VHD | Heat shock protein HSP 90-alpha | / | 0.536 | |
| 4xdm | GDM | Heat shock cognate 90 kDa protein | / | 0.536 | |
| 1yc1 | 4BC | Heat shock protein HSP 90-alpha | / | 0.535 | |
| 2bt0 | CT5 | Heat shock protein HSP 90-alpha | / | 0.535 | |
| 3hz1 | 42C | Heat shock protein HSP 90-alpha | / | 0.534 | |
| 1yet | GDM | Heat shock protein HSP 90-alpha | / | 0.533 | |
| 2wi5 | ZZ5 | Heat shock protein HSP 90-alpha | / | 0.531 | |
| 2vcj | 2EQ | Heat shock protein HSP 90-alpha | / | 0.529 | |
| 4ce1 | 7FK | ATP-dependent molecular chaperone HSP82 | / | 0.528 | |
| 3d2r | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.527 | |
| 2zkj | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.526 | |
| 2yee | 2EC | Heat shock protein HSP 90-alpha | / | 0.525 | |
| 4ivg | ANP | TNF receptor-associated protein 1 | / | 0.525 | |
| 2bre | KJ2 | ATP-dependent molecular chaperone HSP82 | / | 0.523 | |
| 3ekr | PY9 | Heat shock protein HSP 90-alpha | / | 0.523 | |
| 3r4p | FU7 | Heat shock protein HSP 90-alpha | / | 0.523 | |
| 1yc4 | 43P | Heat shock protein HSP 90-alpha | / | 0.522 | |
| 3k99 | PFT | Heat shock protein HSP 90-alpha | / | 0.522 | |
| 4xc0 | ACP | Heat shock cognate 90 kDa protein | / | 0.522 | |
| 4b7p | 9UN | Heat shock protein HSP 90-alpha | / | 0.520 | |
| 2xcm | ADP | Cytosolic heat shock protein 90 | / | 0.518 | |
| 2xht | C0Y | Heat shock protein HSP 90-alpha | / | 0.518 | |
| 1uy7 | PU4 | Heat shock protein HSP 90-alpha | / | 0.517 | |
| 2iwu | NP5 | ATP-dependent molecular chaperone HSP82 | / | 0.517 | |
| 3d0b | SNX | Heat shock protein HSP 90-alpha | / | 0.517 | |
| 1byq | ADP | Heat shock protein HSP 90-alpha | / | 0.515 | |
| 2xd6 | XD6 | ATP-dependent molecular chaperone HSP82 | / | 0.514 | |
| 2yeg | XQG | Heat shock protein HSP 90-alpha | / | 0.514 | |
| 2iws | NP4 | ATP-dependent molecular chaperone HSP82 | / | 0.511 | |
| 2wi1 | ZZ2 | Heat shock protein HSP 90-alpha | / | 0.511 | |
| 1qy8 | RDI | Endoplasmin | / | 0.510 | |
| 2bz5 | AB4 | Heat shock protein HSP 90-alpha | / | 0.510 | |
| 4egh | 0OY | Heat shock protein HSP 90-alpha | / | 0.508 | |
| 4egk | RDC | Heat shock protein HSP 90-alpha | / | 0.508 | |
| 2fyp | RDE | Endoplasmin | / | 0.504 | |
| 2gqp | PA7 | Endoplasmin | / | 0.504 | |
| 2yej | ZZ3 | Heat shock protein HSP 90-alpha | / | 0.504 | |
| 2vw5 | BC6 | ATP-dependent molecular chaperone HSP82 | / | 0.503 | |
| 3rlp | 3RP | Heat shock protein HSP 90-alpha | / | 0.502 | |
| 2xk2 | ADP | Heat shock protein HSP 90-alpha | / | 0.501 | |
| 4egi | B2J | Heat shock protein HSP 90-alpha | / | 0.501 | |
| 4asf | 62U | ATP-dependent molecular chaperone HSP82 | / | 0.500 | |
| 2o1u | ANP | Endoplasmin | / | 0.498 | |
| 3eko | PYU | Heat shock protein HSP 90-alpha | / | 0.497 | |
| 2xx4 | 13I | ATP-dependent molecular chaperone HSP82 | / | 0.496 | |
| 1gjv | AGS | [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial | 2.7.11.4 | 0.494 | |
| 1yc3 | 4BC | Heat shock protein HSP 90-alpha | / | 0.494 | |
| 2esa | GDM | Endoplasmin | / | 0.493 | |
| 3ft5 | MO8 | Heat shock protein HSP 90-alpha | / | 0.493 | |
| 2o1v | ADP | Endoplasmin | / | 0.491 | |
| 2cct | 2E1 | Heat shock protein HSP 90-alpha | / | 0.490 | |
| 3k98 | 1RC | Heat shock protein HSP 90-alpha | / | 0.490 | |
| 3omu | IBD | Heat shock protein 83 | / | 0.490 | |
| 4ce2 | BO5 | ATP-dependent molecular chaperone HSP82 | / | 0.490 | |
| 2wi6 | ZZ6 | Heat shock protein HSP 90-alpha | / | 0.489 | |
| 2yk2 | YJW | Heat shock protein HSP 90-alpha | / | 0.489 | |
| 2ye9 | 2D4 | Heat shock protein HSP 90-alpha | / | 0.487 | |
| 3peh | IBD | Endoplasmin homolog, putative | / | 0.487 | |
| 2xjx | XJX | Heat shock protein HSP 90-alpha | / | 0.486 | |
| 4asg | 814 | ATP-dependent molecular chaperone HSP82 | / | 0.486 | |
| 2zdx | P4A | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.484 | |
| 1z5a | ADP | Type 2 DNA topoisomerase 6 subunit B | / | 0.481 | |
| 3pej | BC2 | Endoplasmin homolog, putative | / | 0.481 | |
| 1nhh | ANP | DNA mismatch repair protein MutL | / | 0.480 | |
| 2cgf | P2N | ATP-dependent molecular chaperone HSP82 | / | 0.478 | |
| 2yei | XQI | Heat shock protein HSP 90-alpha | / | 0.478 | |
| 3hz5 | Z64 | Heat shock protein HSP 90-alpha | / | 0.478 | |
| 2exl | GDM | Endoplasmin | / | 0.477 | |
| 1i59 | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.474 | |
| 3bgr | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.473 | |
| 4r1f | ADP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.472 | |
| 2bu8 | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.471 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.470 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.469 | |
| 2gcg | NDP | Glyoxylate reductase/hydroxypyruvate reductase | 1.1.1.79 | 0.466 | |
| 2vci | 2GJ | Heat shock protein HSP 90-alpha | / | 0.466 | |
| 2xvv | 9DN | Serum albumin | / | 0.466 | |
| 2yi6 | 6QM | Heat shock protein HSP 90-alpha | / | 0.466 | |
| 3say | OFT | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.466 | |
| 4prx | ADP | DNA gyrase subunit B | / | 0.465 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.464 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.463 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.463 | |
| 2f2u | M77 | Rho-associated protein kinase 2 | 2.7.11.1 | 0.462 | |
| 2jf9 | OHT | Estrogen receptor | / | 0.462 | |
| 2xjg | XJG | Heat shock protein HSP 90-alpha | / | 0.462 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.462 | |
| 4mp7 | PFT | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.462 | |
| 2gm1 | 2AZ | Kinesin-like protein KIF11 | / | 0.461 | |
| 3opd | HIE | Heat shock protein 83 | / | 0.461 | |
| 3q5l | KX2 | Heat shock protein 83-1 | / | 0.461 | |
| 2wi2 | ZZ3 | Heat shock protein HSP 90-alpha | / | 0.460 | |
| 2yi7 | BZ8 | Heat shock protein HSP 90-alpha | / | 0.460 | |
| 4e37 | NDP | Catalase | 1.11.1.6 | 0.460 | |
| 1thn | ADP | Anti-sigma F factor | / | 0.459 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.459 | |
| 3mnr | SD1 | Heat shock protein HSP 90-alpha | / | 0.459 | |
| 3zrl | ZRL | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.459 | |
| 1i58 | ADP | Chemotaxis protein CheA | 2.7.13.3 | 0.458 | |
| 3ft8 | MOJ | Heat shock protein HSP 90-alpha | / | 0.458 | |
| 3ozc | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.458 | |
| 2qfo | A13 | Heat shock protein HSP 90-alpha | / | 0.457 | |
| 5hes | 032 | Mitogen-activated protein kinase kinase kinase 20 | 2.7.11.25 | 0.457 | |
| 2yjw | YJW | Heat shock protein HSP 90-alpha | / | 0.456 | |
| 3fp0 | FP0 | 15-O-acetyltransferase | / | 0.456 | |
| 2bsm | BSM | Heat shock protein HSP 90-alpha | / | 0.455 | |
| 2wi7 | 2KL | Heat shock protein HSP 90-alpha | / | 0.454 | |
| 2yec | XQ0 | Heat shock protein HSP 90-alpha | / | 0.454 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.454 | |
| 2vna | NAP | Prostaglandin reductase 2 | 1.3.1.48 | 0.453 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.453 | |
| 4ksh | HTT | DNA gyrase subunit B | / | 0.453 | |
| 5a3c | NAD | SIR2 family protein | / | 0.453 | |
| 2c3k | ABO | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.452 | |
| 2xsz | ATP | RuvB-like 2 | 3.6.4.12 | 0.452 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.451 | |
| 2uwd | 2GG | Heat shock protein HSP 90-alpha | / | 0.451 | |
| 3uag | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.451 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.450 | |
| 1p0f | NAP | NADP-dependent alcohol dehydrogenase | 1.1.1.2 | 0.450 | |
| 1s0z | EB1 | Vitamin D3 receptor | / | 0.450 | |
| 2cah | NDP | Catalase | 1.11.1.6 | 0.450 | |
| 2ycf | YCF | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.450 | |
| 3nie | ANP | Mitogen-activated protein kinase | / | 0.450 | |
| 3ule | C69 | Actin-related protein 3 | / | 0.450 | |
| 1npt | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.449 | |
| 1wwk | NAD | 307aa long hypothetical phosphoglycerate dehydrogenase | / | 0.449 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.449 | |
| 1nm5 | NAP | NAD(P) transhydrogenase subunit beta | 1.6.1.2 | 0.448 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.448 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.448 | |
| 1pvg | ANP | DNA topoisomerase 2 | 5.99.1.3 | 0.447 | |
| 2fwz | H71 | Heat shock protein HSP 90-alpha | / | 0.447 | |
| 2jfg | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.447 | |
| 3c7q | XIN | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.447 | |
| 3ujl | A8S | Abscisic acid receptor PYL2 | / | 0.447 | |
| 4fsr | HKC | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.447 | |
| 1i5c | ADP | Chemotaxis protein CheA | 2.7.13.3 | 0.446 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.446 | |
| 1xal | NAD | 3-dehydroquinate synthase | / | 0.446 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 2xa4 | AZ5 | Tyrosine-protein kinase JAK2 | / | 0.446 | |
| 2y67 | N21 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.446 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.446 | |
| 3d75 | NBB | Pheromone-binding protein ASP1 | / | 0.446 | |
| 3gb2 | G3B | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.446 | |
| 4gyz | D5M | Tyrosyl-DNA phosphodiesterase 2 | 3.1.4 | 0.446 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.446 | |
| 1ea6 | ADP | Mismatch repair endonuclease PMS2 | 3.1 | 0.445 | |
| 1eio | GCH | Gastrotropin | / | 0.445 | |
| 1zxm | ANP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.445 | |
| 2fwy | H64 | Heat shock protein HSP 90-alpha | / | 0.445 | |
| 2hy8 | 1ST | Serine/threonine-protein kinase PAK 1 | 2.7.11.1 | 0.445 | |
| 2vxo | XMP | GMP synthase [glutamine-hydrolyzing] | 6.3.5.2 | 0.445 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.445 | |
| 2ye4 | 2FY | Heat shock protein HSP 90-alpha | / | 0.445 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.445 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.445 | |
| 4nxv | GDP | Mitochondrial dynamics protein MID51 | / | 0.445 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.444 | |
| 1icu | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.444 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 1r0e | DFN | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.444 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.444 | |
| 3th8 | TH9 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.444 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.444 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.444 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.444 | |
| 1jgt | APC | Carboxyethyl-arginine beta-lactam-synthase | 6.3.3.4 | 0.443 | |
| 3g8e | IS1 | Nicotinamide phosphoribosyltransferase | 2.4.2.12 | 0.443 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.443 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.443 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.443 | |
| 4lrz | ADP | PEP-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL | 2.7 | 0.443 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.443 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.442 | |
| 1i58 | ACP | Chemotaxis protein CheA | 2.7.13.3 | 0.442 | |
| 1lhv | NOG | Sex hormone-binding globulin | / | 0.442 | |
| 1mx0 | ANP | Type 2 DNA topoisomerase 6 subunit B | / | 0.442 | |
| 1u3c | FAD | Cryptochrome-1 | / | 0.442 | |
| 2nq8 | ZID | Enoyl-ACP reductase | / | 0.442 | |
| 3a6q | FMN | FMN-binding protein | / | 0.442 | |
| 3c11 | GDM | ATP-dependent molecular chaperone HSP82 | / | 0.442 | |
| 3ncz | 3NC | Rho-associated protein kinase 1 | 2.7.11.1 | 0.442 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.442 | |
| 3zhq | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.442 | |
| 4fsm | HK1 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.442 | |
| 4mle | VO1 | Glucokinase | 2.7.1.2 | 0.442 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.442 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.441 | |
| 1z5c | ADP | Type 2 DNA topoisomerase 6 subunit B | / | 0.441 | |
| 2qoq | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.441 | |
| 2xve | FAD | Putative flavin-containing monooxygenase | / | 0.441 | |
| 3da1 | FAD | Glycerol-3-phosphate dehydrogenase | / | 0.441 | |
| 3neg | PYV | Abscisic acid receptor PYL1 | / | 0.441 | |
| 3tki | S25 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.441 | |
| 3zrm | ZRM | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.441 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.441 | |
| 4nmb | FAD | Bifunctional protein PutA | / | 0.441 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.441 | |
| 5e8w | STU | TGF-beta receptor type-1 | 2.7.11.30 | 0.441 | |
| 1fm7 | DFV | Chalcone--flavonone isomerase 1 | 5.5.1.6 | 0.440 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1nvs | UCM | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.440 | |
| 2aq8 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 2bbq | PFG | Thymidylate synthase | / | 0.440 | |
| 2bxm | IMN | Serum albumin | / | 0.440 | |
| 2rc6 | NAP | Ferredoxin--NADP reductase | / | 0.440 | |
| 2uxp | CLM | HTH-type transcriptional regulator TtgR | / | 0.440 | |
| 2xhx | T5M | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 3e39 | FMN | Nitroreductase | / | 0.440 | |
| 3hwx | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.440 | |
| 3o6o | 94M | Heat shock protein 83 | / | 0.440 | |
| 3sgv | 2BJ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.440 | |
| 4iwo | 1H4 | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.440 |