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 |
|---|---|---|---|
| 3zvu | A8S | Abscisic acid receptor PYR1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3zvu | A8S | Abscisic acid receptor PYR1 | / | 1.000 | |
| 3nmn | PYV | Abscisic acid receptor PYL1 | / | 0.595 | |
| 4lga | A2O | Abscisic acid receptor PYL2 | / | 0.586 | |
| 3kdi | A8S | Abscisic acid receptor PYL2 | / | 0.578 | |
| 3kb3 | A8S | Abscisic acid receptor PYL2 | / | 0.577 | |
| 4jda | A9S | Abscisic acid receptor PYL3 | / | 0.577 | |
| 3ujl | A8S | Abscisic acid receptor PYL2 | / | 0.571 | |
| 3kdj | A8S | Abscisic acid receptor PYL1 | / | 0.569 | |
| 3neg | PYV | Abscisic acid receptor PYL1 | / | 0.566 | |
| 4lg5 | A1O | Abscisic acid receptor PYL2 | / | 0.565 | |
| 3nef | PYV | Abscisic acid receptor PYL1 | / | 0.554 | |
| 3k3k | A8S | Abscisic acid receptor PYR1 | / | 0.553 | |
| 3ns2 | PYV | Abscisic acid receptor PYL2 | / | 0.552 | |
| 4la7 | A1O | Abscisic acid receptor PYL2 | / | 0.551 | |
| 3njo | P2M | Abscisic acid receptor PYR1 | / | 0.548 | |
| 3w9r | A8S | Abscisic acid receptor PYL9 | / | 0.545 | |
| 3k90 | A8S | Abscisic acid receptor PYR1 | / | 0.542 | |
| 3nj0 | PYV | Abscisic acid receptor PYL2 | / | 0.532 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.528 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.518 | |
| 3qn1 | A8S | Abscisic acid receptor PYR1 | / | 0.518 | |
| 4dsc | A8S | Abscisic acid receptor PYL3 | / | 0.517 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.515 | |
| 4ds8 | A8S | Abscisic acid receptor PYL3 | / | 0.515 | |
| 3kb0 | A8S | Abscisic acid receptor PYL2 | / | 0.505 | |
| 4oic | A8S | Bet v I allergen-like | / | 0.504 | |
| 3oji | PYV | Abscisic acid receptor PYL3 | / | 0.497 | |
| 3oqu | A8S | Abscisic acid receptor PYL9 | / | 0.497 | |
| 3r6p | A8S | Abscisic acid receptor PYL10 | / | 0.494 | |
| 4dsb | A8S | Abscisic acid receptor PYL3 | / | 0.491 | |
| 2hl0 | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.485 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.472 | |
| 4mv4 | ACP | Biotin carboxylase | 6.3.4.14 | 0.472 | |
| 1zg3 | 2HI | Isoflavone 4'-O-methyltransferase | / | 0.471 | |
| 3s2a | 2NQ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.469 | |
| 4hnc | 0UT | Mandelate racemase | / | 0.469 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.468 | |
| 1ot7 | CHC | Bile acid receptor | / | 0.467 | |
| 3nmh | PYV | Abscisic acid receptor PYL2 | / | 0.467 | |
| 1e90 | MYC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.466 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.466 | |
| 4tv3 | ML9 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform | / | 0.466 | |
| 4bfr | J82 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit beta isoform | 2.7.1.153 | 0.465 | |
| 4ajw | VWN | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform | 2.7.1.153 | 0.464 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.463 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.463 | |
| 4nmb | FAD | Bifunctional protein PutA | / | 0.463 | |
| 5ack | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.463 | |
| 3nmv | PYV | Abscisic acid receptor PYL2 | / | 0.462 | |
| 4fad | 0TB | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.462 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.462 | |
| 4wzy | ATP | Maltokinase | 2.7.1.175 | 0.462 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.461 | |
| 1uof | PNN | Deacetoxycephalosporin C synthase | 1.14.20.1 | 0.461 | |
| 3ml8 | ML8 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.461 | |
| 1crb | RTL | Retinol-binding protein 1 | / | 0.460 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 4ezk | 0SD | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.460 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.459 | |
| 4pkl | 1GH | Uncharacterized protein | / | 0.459 | |
| 1m8h | 6NI | Nitric oxide synthase, inducible | 1.14.13.39 | 0.457 | |
| 1szm | BI4 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.457 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.457 | |
| 3orz | BI4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.457 | |
| 3sa1 | 6DR | Dihydrofolate reductase | / | 0.457 | |
| 1j39 | UPG | DNA beta-glucosyltransferase | / | 0.456 | |
| 2e98 | B29 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.456 | |
| 4at3 | LTI | BDNF/NT-3 growth factors receptor | 2.7.10.1 | 0.456 | |
| 4l8u | 9AZ | Serum albumin | / | 0.456 | |
| 3qaq | QAQ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.455 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.455 | |
| 5d7q | 4I5 | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.455 | |
| 1e8z | STU | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.454 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 2zjw | REF | Casein kinase II subunit alpha | 2.7.11.1 | 0.454 | |
| 3lfc | Z86 | Mitogen-activated protein kinase 14 | / | 0.454 | |
| 3sa2 | 7DR | Dihydrofolate reductase | / | 0.454 | |
| 4ft7 | H3K | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.454 | |
| 2q7g | CCL | Pyrrolysine--tRNA ligase | / | 0.453 | |
| 3pre | 3RE | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.453 | |
| 3r9n | Z68 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.453 | |
| 4l23 | X6K | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform | / | 0.453 | |
| 3fwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 3meg | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.452 | |
| 4mv8 | ACP | Biotin carboxylase | 6.3.4.14 | 0.452 | |
| 4rqv | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.452 | |
| 2hma | SAM | tRNA-specific 2-thiouridylase MnmA | / | 0.451 | |
| 3qlr | QLR | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1dhi | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.450 | |
| 2feu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.450 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.449 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 1osv | CHC | Bile acid receptor | / | 0.449 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 1so2 | 666 | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.449 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 3jwc | EKB | Dihydrofolate reductase | / | 0.449 | |
| 4egn | TWO | Cytochrome P450 | / | 0.449 | |
| 1e5q | NDP | Saccharopine dehydrogenase [NADP(+), L-glutamate-forming] | 1.5.1.10 | 0.448 | |
| 1kl2 | FON | Serine hydroxymethyltransferase | / | 0.448 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 3iel | U5P | Ribonuclease TTHA0252 | 3.1 | 0.448 | |
| 3l08 | ZIG | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.448 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.448 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 4a51 | DQ8 | Kinesin-like protein KIF11 | / | 0.448 | |
| 4eqc | XR1 | Serine/threonine-protein kinase PAK 1 | 2.7.11.1 | 0.448 | |
| 4ocv | ANP | Aminoglycoside phosphotransferase | / | 0.448 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.448 | |
| 1eet | BFU | Gag-Pol polyprotein | 2.7.7.49 | 0.447 | |
| 1scu | COA | Succinate--CoA ligase [ADP-forming] subunit alpha | 6.2.1.5 | 0.447 | |
| 3eej | 53R | Uncharacterized protein | / | 0.447 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.447 | |
| 4c9p | CAM | Cytochrome P450 | / | 0.447 | |
| 4dk7 | 0KS | Oxysterols receptor LXR-beta | / | 0.447 | |
| 4xdm | GDM | Heat shock cognate 90 kDa protein | / | 0.447 | |
| 1drb | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1m9k | 7NI | Nitric oxide synthase, endothelial | 1.14.13.39 | 0.446 | |
| 2q66 | ATP | Poly(A) polymerase | 2.7.7.19 | 0.446 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.446 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.446 | |
| 4otp | ADP | Serine/threonine-protein kinase RIO1 | 2.7.11.1 | 0.446 | |
| 1xu9 | CPS | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 2hy0 | 306 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.445 | |
| 2vwq | NAP | Glucose 1-dehydrogenase | / | 0.445 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.445 | |
| 4elg | 52J | Dihydrofolate reductase | / | 0.445 | |
| 4pd6 | URI | Nucleoside permease | / | 0.445 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.444 | |
| 1t1r | IMB | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.444 | |
| 2cda | NAP | Glucose 1-dehydrogenase | / | 0.444 | |
| 2chw | 039 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.444 | |
| 2fpc | SCG | Strictosidine synthase | 4.3.3.2 | 0.444 | |
| 2itq | ITQ | Epidermal growth factor receptor | 2.7.10.1 | 0.444 | |
| 2m56 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2zaw | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 3dey | DHT | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 3eem | 53V | Uncharacterized protein | / | 0.444 | |
| 3klm | DHT | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.444 | |
| 4ap1 | NAP | Steroid monooxygenase | / | 0.444 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.444 | |
| 4g21 | 0VP | Vitamin D3 receptor A | / | 0.444 | |
| 4hle | 17V | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.444 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 1h1w | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.443 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2brm | DFZ | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.443 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 3jzf | JZK | Biotin carboxylase | 6.3.4.14 | 0.443 | |
| 3q44 | D50 | M1 family aminopeptidase | 3.4.11 | 0.443 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.443 | |
| 3w5r | LOA | Vitamin D3 receptor | / | 0.443 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.443 | |
| 4ej4 | EJ4 | Delta-type opioid receptor | / | 0.443 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 1kqu | BR4 | Phospholipase A2, membrane associated | / | 0.442 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2zax | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 2ze2 | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.442 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.442 | |
| 3qlz | QLZ | Uncharacterized protein | / | 0.442 | |
| 3u8h | BHP | Phospholipase A2, membrane associated | / | 0.442 | |
| 4fjy | FJY | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.442 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.442 | |
| 4xx9 | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.442 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 1og5 | SWF | Cytochrome P450 2C9 | / | 0.441 | |
| 1qpj | STU | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.441 | |
| 1uu7 | BI2 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.441 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.441 | |
| 2b00 | GCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.441 | |
| 2y30 | SM8 | Putative repressor SimReg2 | / | 0.441 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.441 | |
| 3hz1 | 37D | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 3sqy | Q11 | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 4azw | ATP | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.441 | |
| 4g1d | 0VK | Vitamin D3 receptor A | / | 0.441 | |
| 4h98 | 14Q | Uncharacterized protein | / | 0.441 | |
| 1f5f | DHT | Sex hormone-binding globulin | / | 0.440 | |
| 1fml | RTL | Retinol dehydratase | / | 0.440 | |
| 1fp2 | HMO | Isoflavone-7-O-methyltransferase 8 | 2.1.1.150 | 0.440 | |
| 1n4h | REA | Nuclear receptor ROR-beta | / | 0.440 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.440 | |
| 2a19 | ANP | Interferon-induced, double-stranded RNA-activated protein kinase | 2.7.11.1 | 0.440 | |
| 2a1n | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.440 | |
| 2ph5 | NAD | Homospermidine synthase | / | 0.440 | |
| 2vtt | LZD | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.440 | |
| 2w2l | NAD | D-mandelate dehydrogenase | / | 0.440 | |
| 2y3s | TIR | TamL | / | 0.440 | |
| 3dmj | GWE | Pol protein | / | 0.440 | |
| 3lxi | CAM | Cytochrome P450 | / | 0.440 | |
| 3qly | 55V | Uncharacterized protein | / | 0.440 | |
| 3srq | Q19 | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4l4b | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 4rqk | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.440 | |
| 4ruj | VDX | Vitamin D3 receptor A | / | 0.440 | |
| 4wh3 | ATP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.440 | |
| 5cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 |