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 |
|---|---|---|---|
| 3ls8 | AJZ | Phosphatidylinositol 3-kinase catalytic subunit type 3 | 2.7.1.137 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3ls8 | AJZ | Phosphatidylinositol 3-kinase catalytic subunit type 3 | 2.7.1.137 | 1.000 | |
| 4l23 | X6K | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform | / | 0.570 | |
| 4fad | 0TB | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.569 | |
| 3s2a | 2NQ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.549 | |
| 4flh | 14K | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.549 | |
| 4l2y | XXK | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform | / | 0.543 | |
| 3ml9 | ML9 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.536 | |
| 4gb9 | 0WR | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.530 | |
| 4ezj | 0SC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.523 | |
| 3l08 | ZIG | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.522 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.522 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.522 | |
| 3qk0 | QK0 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.519 | |
| 1e7v | LY2 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.518 | |
| 3w0p | ADP | Hygromycin-B 4-O-kinase | 2.7.1.163 | 0.517 | |
| 4fjy | FJY | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.517 | |
| 2v4l | ABJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.513 | |
| 4ezk | 0SD | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.513 | |
| 4hle | 17V | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.513 | |
| 2chz | 093 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.510 | |
| 4wh3 | ATP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.509 | |
| 4hvb | 19P | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.508 | |
| 4anv | 751 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.507 | |
| 4f1s | F1S | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.507 | |
| 3zw3 | ZW3 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.504 | |
| 2a5u | QYT | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.501 | |
| 4anu | EM7 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.496 | |
| 4izy | 1J2 | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.496 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.495 | |
| 4ajw | VWN | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform | 2.7.1.153 | 0.494 | |
| 4fhk | 0U0 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.494 | |
| 3ml8 | ML8 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.493 | |
| 4dk5 | 0KO | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.493 | |
| 3gc9 | B45 | Mitogen-activated protein kinase 11 | 2.7.11.24 | 0.490 | |
| 1e90 | MYC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.489 | |
| 3apf | BMW | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.488 | |
| 4fhj | 0TZ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.486 | |
| 4ezl | 0SE | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.485 | |
| 3w0s | ANP | Hygromycin-B 4-O-kinase | 2.7.1.163 | 0.483 | |
| 4bfr | J82 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit beta isoform | 2.7.1.153 | 0.483 | |
| 1e8z | STU | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.481 | |
| 2a4z | BYM | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.481 | |
| 4hyu | 1BK | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.480 | |
| 4tv3 | ML9 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform | / | 0.480 | |
| 3pre | 3RE | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.479 | |
| 4anw | O92 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.479 | |
| 4kz0 | 1UJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.479 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.478 | |
| 4dit | 0KD | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.477 | |
| 4j6i | 1JV | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.476 | |
| 3pjc | PJC | Tyrosine-protein kinase JAK3 | 2.7.10.2 | 0.474 | |
| 4ful | 0VU | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.473 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.471 | |
| 4mcv | 29K | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.471 | |
| 3hu2 | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.470 | |
| 3qaq | QAQ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.470 | |
| 1q3d | STU | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.469 | |
| 1qxl | FR8 | Adenosine deaminase | 3.5.4.4 | 0.468 | |
| 4bcm | T7Z | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.467 | |
| 5ap5 | 7RO | Dual specificity protein kinase TTK | 2.7.12.1 | 0.467 | |
| 2buj | STU | Serine/threonine-protein kinase 16 | / | 0.466 | |
| 4o4f | ATP | Kinase | / | 0.466 | |
| 1lhv | NOG | Sex hormone-binding globulin | / | 0.464 | |
| 2fpc | SCG | Strictosidine synthase | 4.3.3.2 | 0.464 | |
| 3a4o | STU | Tyrosine-protein kinase Lyn | 2.7.10.2 | 0.464 | |
| 4b8l | A0P | Aurora kinase B-A | 2.7.11.1 | 0.464 | |
| 4hys | 1BJ | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.463 | |
| 1phg | MYT | Camphor 5-monooxygenase | 1.14.15.1 | 0.462 | |
| 3ibe | L64 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.462 | |
| 3w0n | ANP | Hygromycin-B 4-O-kinase | 2.7.1.163 | 0.462 | |
| 4eos | 1RO | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.462 | |
| 1h1w | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.461 | |
| 4jia | 1K3 | Tyrosine-protein kinase JAK2 | / | 0.461 | |
| 2o65 | MYF | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.460 | |
| 3lj3 | WYE | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.460 | |
| 3ztx | ZTX | Aurora kinase B-A | 2.7.11.1 | 0.460 | |
| 3rus | ADP | Chaperonin | / | 0.459 | |
| 2pyw | ADP | Methylthioribose kinase | 2.7.1.100 | 0.458 | |
| 3mfr | ANP | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.458 | |
| 4fsr | HKC | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.458 | |
| 1n71 | COA | Aac(6')-Ii protein | / | 0.457 | |
| 4i0r | 1B4 | Tyrosine-protein kinase SYK | 2.7.10.2 | 0.457 | |
| 1zrz | BI1 | Protein kinase C iota type | 2.7.11.13 | 0.456 | |
| 2chw | 039 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.456 | |
| 3dzd | ADP | Transcriptional regulator (NtrC family) | / | 0.456 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.456 | |
| 2w98 | P1Z | Prostaglandin reductase 2 | 1.3.1.48 | 0.455 | |
| 2ycs | NXP | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.455 | |
| 3a99 | ANP | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.455 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.455 | |
| 1uu7 | BI2 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.454 | |
| 2hxl | 422 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.454 | |
| 2vd5 | BI8 | Myotonin-protein kinase | 2.7.11.1 | 0.454 | |
| 2ydi | YDI | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.454 | |
| 2yit | YIT | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.454 | |
| 4wh2 | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.454 | |
| 1qpj | STU | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.453 | |
| 1ykd | CMP | Adenylate cyclase | / | 0.453 | |
| 3hav | ATP | Aminoglycoside phosphotransferase | / | 0.453 | |
| 3nx4 | NAP | Putative oxidoreductase | / | 0.453 | |
| 4mv4 | ACP | Biotin carboxylase | 6.3.4.14 | 0.453 | |
| 4xwt | U5P | Ribonuclease J | / | 0.453 | |
| 2hy8 | 1ST | Serine/threonine-protein kinase PAK 1 | 2.7.11.1 | 0.452 | |
| 3t8o | ATP | Rhodopsin kinase | / | 0.452 | |
| 4h98 | 14Q | Uncharacterized protein | / | 0.452 | |
| 4xf7 | ACP | Carbohydrate/pyrimidine kinase, PfkB family | / | 0.452 | |
| 2etr | Y27 | Rho-associated protein kinase 1 | 2.7.11.1 | 0.451 | |
| 3r6p | A8S | Abscisic acid receptor PYL10 | / | 0.451 | |
| 5c8y | ACP | Tubulin tyrosine ligase | / | 0.451 | |
| 1e8w | QUE | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 2xm9 | LWH | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.450 | |
| 3dpd | 41A | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 4fr4 | STU | Serine/threonine-protein kinase 32A | 2.7.11.1 | 0.450 | |
| 4j97 | ACP | Fibroblast growth factor receptor 2 | / | 0.450 | |
| 4ock | ANP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.450 | |
| 4qml | ANP | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.450 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 3igo | ANP | Calmodulin-domain protein kinase 1, putative | / | 0.449 | |
| 3tnw | F18 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.449 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.449 | |
| 4bcp | T3C | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.449 | |
| 4cav | MYA | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.449 | |
| 4jv6 | 18F | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.449 | |
| 4zol | ACP | Tubulin tyrosine ligase | / | 0.449 | |
| 5auw | QUE | Death-associated protein kinase 1 | 2.7.11.1 | 0.449 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.448 | |
| 3zew | STU | Ephrin type-B receptor 4 | 2.7.10.1 | 0.448 | |
| 4l9k | EHF | Serum albumin | / | 0.448 | |
| 4m49 | 22Y | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.448 | |
| 4rqk | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.448 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.448 | |
| 4yhj | AN2 | G protein-coupled receptor kinase 4 | 2.7.11.16 | 0.448 | |
| 1iwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 1lhw | ESM | Sex hormone-binding globulin | / | 0.447 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.447 | |
| 1zzl | TZY | Mitogen-activated protein kinase 14 | / | 0.447 | |
| 2vr1 | ATF | Biotin carboxylase | 6.3.4.14 | 0.447 | |
| 2wle | COA | Polysialic acid O-acetyltransferase | / | 0.447 | |
| 3l8s | BFF | Mitogen-activated protein kinase 14 | / | 0.447 | |
| 3zvv | XAZ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.447 | |
| 4c34 | STU | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.447 | |
| 4hne | ADP | Phosphatidylinositol 4-kinase type 2-alpha | / | 0.447 | |
| 4uya | AGS | Mitogen-activated protein kinase kinase kinase 21 | 2.7.11.25 | 0.447 | |
| 5dc5 | B3N | Histone deacetylase 8 | 3.5.1.98 | 0.447 | |
| 5kgp | ACO | Predicted acetyltransferase | / | 0.447 | |
| 1tl1 | H18 | Gag-Pol polyprotein | 2.7.7.49 | 0.446 | |
| 3lfc | Z86 | Mitogen-activated protein kinase 14 | / | 0.446 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.446 | |
| 3ua5 | 06X | Cytochrome P450 2B6 | 1.14.13 | 0.446 | |
| 4d0l | 093 | Phosphatidylinositol 4-kinase beta | 2.7.1.67 | 0.446 | |
| 1t87 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.445 | |
| 2xs0 | ANP | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.445 | |
| 3uvq | FS8 | Mitogen-activated protein kinase 14 | / | 0.445 | |
| 4agu | D15 | Cyclin-dependent kinase-like 1 | / | 0.445 | |
| 4eol | 1RO | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.445 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.445 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.445 | |
| 4ic7 | ANP | Mitogen-activated protein kinase 7 | 2.7.11.24 | 0.445 | |
| 4jq8 | KJ8 | Epidermal growth factor receptor | 2.7.10.1 | 0.445 | |
| 4ubu | COA | Steroid 3-ketoacyl-CoA thiolase | / | 0.445 | |
| 4wzy | ATP | Maltokinase | 2.7.1.175 | 0.445 | |
| 2dq7 | STU | Tyrosine-protein kinase Fyn | 2.7.10.2 | 0.444 | |
| 2hw2 | RFP | Rifampin ADP-ribosyl transferase | / | 0.444 | |
| 3awh | FMN | FMN-binding protein | / | 0.444 | |
| 3l8p | 0CE | Angiopoietin-1 receptor | 2.7.10.1 | 0.444 | |
| 3neg | PYV | Abscisic acid receptor PYL1 | / | 0.444 | |
| 3qtr | X36 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.444 | |
| 4ho8 | THM | Glucose-1-phosphate thymidylyltransferase | / | 0.444 | |
| 5auz | GEN | Death-associated protein kinase 1 | 2.7.11.1 | 0.444 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 4azw | ATP | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.443 | |
| 4dca | ADP | Aminoglycoside phosphotransferase | / | 0.443 | |
| 4nka | 2K7 | Fibroblast growth factor receptor 1 | / | 0.443 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.443 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 2c5y | MTW | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.442 | |
| 2izr | BRK | Casein kinase I isoform gamma-3 | 2.7.11.1 | 0.442 | |
| 2izs | BRQ | Casein kinase I isoform gamma-3 | 2.7.11.1 | 0.442 | |
| 4c4f | 7CE | Dual specificity protein kinase TTK | 2.7.12.1 | 0.442 | |
| 4n57 | ADP | APH(2'')-Id | / | 0.442 | |
| 4qmx | H8H | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.442 | |
| 5av4 | GEN | Death-associated protein kinase 1 | 2.7.11.1 | 0.442 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.442 | |
| 2i51 | FMN | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding | / | 0.441 | |
| 2pe1 | 517 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.441 | |
| 2yiq | YIQ | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.441 | |
| 3q2m | CKI | Spectinomycin phosphotransferase | / | 0.441 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.441 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.441 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.440 | |
| 3i4b | Z48 | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.440 | |
| 3iel | U5P | Ribonuclease TTHA0252 | 3.1 | 0.440 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.440 | |
| 3my5 | RFZ | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.440 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.440 | |
| 4iwo | 1H4 | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.440 | |
| 3rey | XAC | Adenosine receptor A2a | / | 0.440 |