sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4fhy | 3AT | Terminal uridylyltransferase cid1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4fhy | 3AT | Terminal uridylyltransferase cid1 | / | 1.000 | |
| 4fhp | UTP | Terminal uridylyltransferase cid1 | / | 0.596 | |
| 2q0c | CTP | Poly(A) polymerase, putative | / | 0.527 | |
| 2q0g | UPU | Poly(A) polymerase, putative | / | 0.497 | |
| 3ed1 | GA3 | Gibberellin receptor GID1 | / | 0.488 | |
| 2b51 | UTP | RNA editing complex protein MP57 | / | 0.487 | |
| 3zu2 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.480 | |
| 2z4s | ADP | Chromosomal replication initiator protein DnaA | / | 0.479 | |
| 2ikf | UTP | Poly(A) polymerase, putative | / | 0.473 | |
| 4ffr | ATP | Uncharacterized protein | / | 0.472 | |
| 1ols | TDP | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.471 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.471 | |
| 4lga | A2O | Abscisic acid receptor PYL2 | / | 0.470 | |
| 4xvr | GNP | GTPase HRas | / | 0.469 | |
| 2itq | ITQ | Epidermal growth factor receptor | 2.7.10.1 | 0.467 | |
| 2yx6 | ADP | Uncharacterized protein | / | 0.467 | |
| 3a8w | ATP | Protein kinase C iota type | 2.7.11.13 | 0.467 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.467 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.466 | |
| 4aw0 | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.466 | |
| 2q0d | ATP | Poly(A) polymerase, putative | / | 0.465 | |
| 4ku2 | MYA | 3-oxoacyl-[ACP] synthase III | / | 0.465 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.463 | |
| 1e1q | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.462 | |
| 2nom | DUT | Poly(A) polymerase, putative | / | 0.462 | |
| 4fgc | PQ0 | NADPH-dependent 7-cyano-7-deazaguanine reductase | 1.7.1.13 | 0.462 | |
| 4u0m | GTP | Cyclic GMP-AMP synthase | / | 0.461 | |
| 2fpc | SCG | Strictosidine synthase | 4.3.3.2 | 0.460 | |
| 3nmv | PYV | Abscisic acid receptor PYL2 | / | 0.460 | |
| 4u0s | ADP | Adenosine monophosphate-protein transferase FICD | 2.7.7.n1 | 0.460 | |
| 4c36 | ZO9 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.459 | |
| 5a30 | AGS | Mitochondrial poly(A) polymerase | / | 0.459 | |
| 5hwr | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.458 | |
| 1cs4 | FOK | Adenylate cyclase type 2 | / | 0.457 | |
| 1cs4 | FOK | Adenylate cyclase type 5 | / | 0.457 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.457 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.457 | |
| 4ie0 | PD2 | Alpha-ketoglutarate-dependent dioxygenase FTO | / | 0.457 | |
| 1g2v | TTP | Glucose-1-phosphate thymidylyltransferase | / | 0.456 | |
| 1yrx | FMN | AppA protein | / | 0.456 | |
| 2v5a | LZL | Biotin carboxylase | 6.3.4.14 | 0.456 | |
| 4kxl | 6C6 | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 | / | 0.456 | |
| 1ykd | CMP | Adenylate cyclase | / | 0.455 | |
| 4ap1 | NAP | Steroid monooxygenase | / | 0.455 | |
| 4fhf | 0TT | Spore photoproduct lyase | / | 0.455 | |
| 4i8v | BHF | Cytochrome P450 1A1 | 1.14.14.1 | 0.455 | |
| 4jc5 | 1K5 | Stimulator of interferon genes protein | / | 0.455 | |
| 1h9z | RWF | Serum albumin | / | 0.454 | |
| 1tg2 | H2B | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.454 | |
| 2ipj | FFA | Aldo-keto reductase family 1 member C2 | / | 0.454 | |
| 1piw | NAP | NADP-dependent alcohol dehydrogenase 6 | 1.1.1.2 | 0.453 | |
| 3l9n | L9N | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.453 | |
| 3q2j | CKI | Aminoglycoside 3'-phosphotransferase | 2.7.1.95 | 0.453 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.453 | |
| 4yus | FMN | Family 3 adenylate cyclase | / | 0.453 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.453 | |
| 1i24 | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.452 | |
| 2bxq | IMN | Serum albumin | / | 0.452 | |
| 2rge | GNP | GTPase HRas | / | 0.452 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 4dxa | GSP | Ras-related protein Rap-1b | / | 0.452 | |
| 4ib3 | ADP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.452 | |
| 1n5q | TNC | ActVA 6 protein | / | 0.451 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.451 | |
| 2itp | AEE | Epidermal growth factor receptor | 2.7.10.1 | 0.451 | |
| 2rto | IMI | Streptavidin | / | 0.451 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.451 | |
| 2xau | ADP | Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 | 3.6.4.13 | 0.451 | |
| 2zsi | GA4 | Gibberellin receptor GID1A | 3 | 0.451 | |
| 4cf7 | ADP | Adenylate kinase | / | 0.451 | |
| 4jq3 | ZOM | Aldo-keto reductase family 1 member C2 | / | 0.451 | |
| 4jxh | HRC | Cytohesin-2 | / | 0.451 | |
| 1e90 | MYC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 1f5f | DHT | Sex hormone-binding globulin | / | 0.450 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
| 2brh | DFW | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.450 | |
| 2c3y | HTL | Pyruvate synthase | / | 0.450 | |
| 3kdi | A8S | Abscisic acid receptor PYL2 | / | 0.450 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.450 | |
| 4jzr | 4JR | Egl nine homolog 1 | / | 0.450 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1srf | MTB | Streptavidin | / | 0.449 | |
| 2fhn | BNI | Avidin-related protein 4/5 | / | 0.449 | |
| 3d3p | 20A | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.449 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.449 | |
| 4eer | FMN | Phototropin-2 | 2.7.11.1 | 0.449 | |
| 4h5t | ADP | Heat shock cognate 71 kDa protein | / | 0.449 | |
| 4iwq | 1FV | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.449 | |
| 1pr5 | TBN | Purine nucleoside phosphorylase DeoD-type | / | 0.448 | |
| 2f4j | VX6 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.448 | |
| 2q0f | UTP | Poly(A) polymerase, putative | / | 0.448 | |
| 3lfm | 3DT | Alpha-ketoglutarate-dependent dioxygenase FTO | / | 0.448 | |
| 3o57 | ZG2 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.448 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 4mv1 | ADP | Biotin carboxylase | 6.3.4.14 | 0.448 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.447 | |
| 1u71 | MXA | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1vcf | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.447 | |
| 3idc | ANP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.447 | |
| 3ns2 | PYV | Abscisic acid receptor PYL2 | / | 0.447 | |
| 3qiz | QI2 | Botulinum neurotoxin type A | 3.4.24.69 | 0.447 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.447 | |
| 4mvh | 2F5 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.447 | |
| 4njo | NAD | D-3-phosphoglycerate dehydrogenase, putative | / | 0.447 | |
| 1e2j | THM | Thymidine kinase | / | 0.446 | |
| 1mei | MOA | Inosine-5'-monophosphate dehydrogenase | / | 0.446 | |
| 1x7b | 041 | Estrogen receptor beta | / | 0.446 | |
| 2c94 | TSF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.446 | |
| 3b1d | PLS | BetaC-S lyase | / | 0.446 | |
| 3ebl | GA4 | Gibberellin receptor GID1 | / | 0.446 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.446 | |
| 3nmn | PYV | Abscisic acid receptor PYL1 | / | 0.446 | |
| 3w5e | NVW | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.446 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.446 | |
| 4lsl | 1YQ | Gag-Pol polyprotein | 2.7.7.49 | 0.446 | |
| 5ack | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.446 | |
| 1y2d | 4DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 2chz | 093 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.445 | |
| 2erz | HFS | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.445 | |
| 2qqf | A1R | NAD-dependent protein deacetylase HST2 | 3.5.1 | 0.445 | |
| 2uza | HTL | Pyruvate synthase | / | 0.445 | |
| 2xbj | XBJ | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.445 | |
| 2zsh | GA3 | Gibberellin receptor GID1A | 3 | 0.445 | |
| 3o56 | ZG1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.445 | |
| 4fhd | 0TT | Spore photoproduct lyase | / | 0.445 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.445 | |
| 1lke | DOG | Bilin-binding protein | / | 0.444 | |
| 1ro9 | 8BR | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.444 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.444 | |
| 1x0p | FAD | Tll0078 protein | / | 0.444 | |
| 3djf | BC3 | Purine nucleoside phosphorylase | / | 0.444 | |
| 3jpu | TY4 | Transcriptional activator protein LasR | / | 0.444 | |
| 4ho8 | THM | Glucose-1-phosphate thymidylyltransferase | / | 0.444 | |
| 4tx9 | AMZ | Phosphoribosyl isomerase A | / | 0.444 | |
| 1e7v | LY2 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 2aky | AP5 | Adenylate kinase | / | 0.443 | |
| 2toh | HBI | Tyrosine 3-monooxygenase | 1.14.16.2 | 0.443 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.443 | |
| 4l43 | 5FI | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.443 | |
| 1nd5 | 2BF | Prostatic acid phosphatase | 3.1.3.2 | 0.442 | |
| 1nen | DNT | Succinate dehydrogenase iron-sulfur subunit | 1.3.5.1 | 0.442 | |
| 1nen | DNT | Succinate dehydrogenase cytochrome b556 subunit | / | 0.442 | |
| 1s4e | ADP | Galactokinase | / | 0.442 | |
| 2g1m | 4HG | Egl nine homolog 1 | / | 0.442 | |
| 3c14 | FOK | Adenylate cyclase type 2 | / | 0.442 | |
| 3c14 | FOK | Adenylate cyclase type 5 | / | 0.442 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 4ddr | MMV | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 4feu | 537 | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.442 | |
| 4iz0 | 2BI | Genome polyprotein | 2.7.7.48 | 0.442 | |
| 4ku5 | DCC | 3-oxoacyl-[ACP] synthase III | / | 0.442 | |
| 1f9a | ATP | Nicotinamide-nucleotide adenylyltransferase | / | 0.441 | |
| 2a9z | 26A | Adenosine kinase | 2.7.1.20 | 0.441 | |
| 2b8j | ADN | Class B acid phosphatase | 3.1.3.2 | 0.441 | |
| 2bdf | 24A | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.441 | |
| 2brg | DFY | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.441 | |
| 2q0f | U5P | Poly(A) polymerase, putative | / | 0.441 | |
| 2w6z | L21 | Biotin carboxylase | 6.3.4.14 | 0.441 | |
| 3c36 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.441 | |
| 3dol | GWI | Pol protein | / | 0.441 | |
| 3e92 | G6A | Mitogen-activated protein kinase 14 | / | 0.441 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.441 | |
| 4g2f | C07 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.441 | |
| 4jq7 | KJQ | Epidermal growth factor receptor | 2.7.10.1 | 0.441 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.441 | |
| 1a8r | GTP | GTP cyclohydrolase 1 | 3.5.4.16 | 0.440 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1xdu | SFG | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.440 | |
| 2j0s | ANP | Eukaryotic initiation factor 4A-III | 3.6.4.13 | 0.440 | |
| 2v59 | LZK | Biotin carboxylase | 6.3.4.14 | 0.440 | |
| 3e8e | G98 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 3nuu | JOZ | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.440 | |
| 3u2m | FAD | FAD-linked sulfhydryl oxidase ALR | 1.8.3.2 | 0.440 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.440 | |
| 4rrv | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.440 | |
| 4ytn | FD8 | Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial | / | 0.440 | |
| 4ytn | FD8 | Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial | / | 0.440 | |
| 4ytn | FD8 | Succinate dehydrogenase cytochrome b560 | / | 0.440 |