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 |
|---|---|---|---|
| 4cry | ACO | PanD regulatory factor |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4cry | ACO | PanD regulatory factor | / | 1.000 | |
| 4cs0 | ACO | PanD regulatory factor | / | 0.631 | |
| 4crz | ACO | PanD regulatory factor | / | 0.614 | |
| 4mxe | ACO | N-acetyltransferase ESCO1 | 2.3.1 | 0.564 | |
| 4ag7 | COA | Glucosamine 6-phosphate N-acetyltransferase | / | 0.538 | |
| 4hkf | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.530 | |
| 1n71 | COA | Aac(6')-Ii protein | / | 0.527 | |
| 2wpx | ACO | Orf14 | / | 0.525 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.517 | |
| 2wpw | ACO | Orf14 | / | 0.515 | |
| 2ob0 | ACO | N-alpha-acetyltransferase 50 | / | 0.506 | |
| 3vwd | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.506 | |
| 4b5o | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.506 | |
| 4ajw | VWN | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform | 2.7.1.153 | 0.503 | |
| 1j4j | ACO | Acetyltransferase | 2.3.1 | 0.501 | |
| 4fad | 0TB | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.501 | |
| 1fdu | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.499 | |
| 3f0a | ACO | Spermidine N(1)-acetyltransferase | / | 0.497 | |
| 1ghe | ACO | Acetyltransferase | 2.3.1 | 0.495 | |
| 4gs4 | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.493 | |
| 2cy2 | ACO | Probable acetyltransferase | / | 0.492 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.492 | |
| 3tfy | COA | N-alpha-acetyltransferase 50 | 2.3.1 | 0.491 | |
| 2a4n | COA | Aac(6')-Ii protein | / | 0.488 | |
| 3vwe | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.484 | |
| 4jv6 | 18F | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.484 | |
| 4u9v | ACO | N-alpha-acetyltransferase 40 | 2.3.1 | 0.484 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.482 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.481 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.479 | |
| 2k5t | COA | PanD regulatory factor | / | 0.478 | |
| 4b5p | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.476 | |
| 3uzc | T4E | Adenosine receptor A2a | / | 0.475 | |
| 1p0h | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.474 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.474 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.472 | |
| 4jvb | 1M0 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.472 | |
| 4anu | EM7 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.471 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.469 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.469 | |
| 5kf2 | COA | Predicted acetyltransferase | / | 0.469 | |
| 1b87 | ACO | Aac(6')-Ii protein | / | 0.468 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.468 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.468 | |
| 4h6z | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.468 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.467 | |
| 3ml8 | ML8 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.467 | |
| 3wow | ANP | Casein kinase II subunit alpha | 2.7.11.1 | 0.466 | |
| 4u9y | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.466 | |
| 1daj | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 2c27 | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.465 | |
| 4hvb | 19P | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.465 | |
| 5kgh | ACO | Predicted acetyltransferase | / | 0.465 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.464 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.464 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.464 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.464 | |
| 4f1s | F1S | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.464 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 4if5 | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.462 | |
| 1jtu | LYB | Thymidylate synthase | / | 0.461 | |
| 1e90 | MYC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.460 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.460 | |
| 5kgp | ACO | Predicted acetyltransferase | / | 0.460 | |
| 1e8x | ATP | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.459 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.459 | |
| 1jut | LYD | Thymidylate synthase | / | 0.458 | |
| 1pkd | UCN | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.458 | |
| 2bbq | PFG | Thymidylate synthase | / | 0.458 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 2psw | COA | N-alpha-acetyltransferase 50 | / | 0.458 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.458 | |
| 1mb9 | ATP | Carboxyethyl-arginine beta-lactam-synthase | 6.3.3.4 | 0.457 | |
| 1q5d | EPB | Epothilone C/D epoxidase | 1.14 | 0.457 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 4gb9 | 0WR | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.457 | |
| 4l23 | X6K | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform | / | 0.457 | |
| 1iyz | NDP | Probable quinone oxidoreductase | / | 0.456 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.456 | |
| 2a4z | BYM | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.456 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.456 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.456 | |
| 1ewy | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.455 | |
| 1o8c | NDP | Probable acrylyl-CoA reductase AcuI | 1.3.1.84 | 0.455 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.455 | |
| 1zpr | CB3 | Thymidylate synthase | / | 0.455 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.455 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 2a5u | QYT | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.454 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.454 | |
| 2j4z | 626 | Aurora kinase A | 2.7.11.1 | 0.453 | |
| 3tk3 | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.453 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.453 | |
| 4jvf | 17X | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.453 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.453 | |
| 4nmb | FAD | Bifunctional protein PutA | / | 0.453 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.452 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.452 | |
| 3f8k | COA | Uncharacterized protein | / | 0.452 | |
| 1kgj | FL8 | Transthyretin | / | 0.451 | |
| 2x7b | COA | N-alpha-acetyltransferase | 2.3.1 | 0.451 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.451 | |
| 3s2a | 2NQ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.451 | |
| 4h6u | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.451 | |
| 1juj | LYA | Thymidylate synthase | 2.1.1.45 | 0.450 | |
| 2og8 | 1N8 | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.450 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.450 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.450 | |
| 4ezj | 0SC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 4fa6 | 0TA | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 4hle | 17V | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 1dgm | ADN | Adenosine kinase | 2.7.1.20 | 0.449 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2fzi | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 2iw8 | 4SP | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.449 | |
| 3c1x | CKK | Hepatocyte growth factor receptor | 2.7.10.1 | 0.449 | |
| 3qaq | QAQ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.449 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.449 | |
| 4ocv | ANP | Aminoglycoside phosphotransferase | / | 0.449 | |
| 1f28 | F89 | Thymidylate synthase | 2.1.1.45 | 0.448 | |
| 1o5r | FR9 | Adenosine deaminase | 3.5.4.4 | 0.448 | |
| 3kyt | HC2 | Nuclear receptor ROR-gamma | / | 0.448 | |
| 3mfr | ANP | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.448 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.448 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 4g21 | 0VP | Vitamin D3 receptor A | / | 0.448 | |
| 4ua3 | COA | N-alpha-acetyltransferase 40 | 2.3.1 | 0.448 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.448 | |
| 1cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1ot7 | CHC | Bile acid receptor | / | 0.447 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.447 | |
| 3amy | AGI | Casein kinase II subunit alpha | 2.7.11.1 | 0.447 | |
| 3nx4 | NAP | Putative oxidoreductase | / | 0.447 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.447 | |
| 4kxn | 6K6 | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 | / | 0.447 | |
| 5kf2 | ACO | Predicted acetyltransferase | / | 0.447 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.446 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 4bkj | STI | Epithelial discoidin domain-containing receptor 1 | 2.7.10.1 | 0.446 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.446 | |
| 4u97 | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.446 | |
| 1n4h | REA | Nuclear receptor ROR-beta | / | 0.445 | |
| 2nom | DUT | Poly(A) polymerase, putative | / | 0.445 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.445 | |
| 3dga | RJ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.445 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4l3l | 5FI | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.445 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.444 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.444 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.444 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.444 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.444 | |
| 3ls8 | AJZ | Phosphatidylinositol 3-kinase catalytic subunit type 3 | 2.7.1.137 | 0.444 | |
| 3wix | LC3 | Induced myeloid leukemia cell differentiation protein Mcl-1 | / | 0.444 | |
| 4bch | T7Z | Cyclin-dependent kinase 9 | 2.7.11.22 | 0.444 | |
| 5ckw | ANP | Uncharacterized protein | / | 0.444 | |
| 1rd4 | L08 | Integrin alpha-L | / | 0.443 | |
| 1syn | F89 | Thymidylate synthase | / | 0.443 | |
| 2chw | 039 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.443 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.443 | |
| 3k3b | ADP | Kinesin-like protein KIF11 | / | 0.443 | |
| 3ml9 | ML9 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 3mqe | 416 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.443 | |
| 3up0 | D7S | aceDAF-12 | / | 0.443 | |
| 3vru | YS3 | Vitamin D3 receptor | / | 0.443 | |
| 3zc3 | NAP | Ferredoxin--NADP reductase | 1.18.1.2 | 0.443 | |
| 4qkn | JMS | Alpha-ketoglutarate-dependent dioxygenase FTO | / | 0.443 | |
| 1byg | STU | Tyrosine-protein kinase CSK | / | 0.442 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2bfp | H4B | Pteridine reductase 1 | 1.5.1.33 | 0.442 | |
| 2vu3 | LZE | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.442 | |
| 3r9h | Z67 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.442 | |
| 4b99 | R4L | Mitogen-activated protein kinase 7 | 2.7.11.24 | 0.442 | |
| 4bcq | TJF | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.442 | |
| 4cav | MYA | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.442 | |
| 4ogr | ADN | Cyclin-dependent kinase 9 | 2.7.11.22 | 0.442 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.442 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.441 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 3cv9 | VDX | Vitamin D3 dihydroxylase | / | 0.441 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.441 | |
| 4eev | L1X | Hepatocyte growth factor receptor | 2.7.10.1 | 0.441 | |
| 1fml | RTL | Retinol dehydratase | / | 0.440 | |
| 1ju6 | LYA | Thymidylate synthase | 2.1.1.45 | 0.440 | |
| 1zdw | FLV | Prenyltransferase | / | 0.440 | |
| 2g2h | P16 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.440 | |
| 3bqd | DAY | Glucocorticoid receptor | / | 0.440 | |
| 3cth | 319 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.440 | |
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.440 | |
| 3w5t | LHP | Vitamin D3 receptor | / | 0.440 | |
| 4bb5 | HD2 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.440 | |
| 4iwx | ADP | Ribosomal protein S6--L-glutamate ligase | / | 0.440 | |
| 4j26 | EST | Estrogen receptor beta | / | 0.440 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.440 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.440 | |
| 5doz | NDP | JamJ | / | 0.440 | |
| 5iua | 6DX | Adenosine receptor A2a | / | 0.440 |