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 |
|---|---|---|---|
| 3dhk | 23U | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3dhk | 23U | Prothrombin | 3.4.21.5 | 1.000 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.797 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.785 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.770 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.749 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.742 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.742 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.736 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.723 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.721 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.711 | |
| 3egk | M18 | Prothrombin | 3.4.21.5 | 0.710 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.703 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.691 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.687 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.687 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.686 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.681 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.678 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.675 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.675 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.669 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.661 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.658 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.658 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.650 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.649 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.649 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.647 | |
| 1ypg | UIR | Prothrombin | 3.4.21.5 | 0.644 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.644 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.642 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.638 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.637 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.632 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.632 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.631 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.631 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.629 | |
| 3f68 | 91U | Prothrombin | 3.4.21.5 | 0.628 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.626 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.624 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.621 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.621 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.620 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.619 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.619 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.617 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.616 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.616 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.615 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.613 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.612 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.610 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.609 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.609 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.605 | |
| 2jh0 | 701 | Prothrombin | 3.4.21.5 | 0.603 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.603 | |
| 2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.600 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.597 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.596 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.594 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.592 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.592 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.589 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.588 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.587 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.585 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.584 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.583 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.582 | |
| 1c5n | ESI | Prothrombin | 3.4.21.5 | 0.582 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.582 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.581 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.578 | |
| 1kts | C24 | Prothrombin | 3.4.21.5 | 0.576 | |
| 2cn0 | F25 | Prothrombin | 3.4.21.5 | 0.575 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.574 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.570 | |
| 4hfp | 15U | Prothrombin | 3.4.21.5 | 0.570 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.568 | |
| 1uvs | I11 | Prothrombin | 3.4.21.5 | 0.567 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.567 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.567 | |
| 2a2x | NA9 | Prothrombin | 3.4.21.5 | 0.566 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.565 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.565 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.565 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.565 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.563 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.561 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.561 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.556 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.552 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.551 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.548 | |
| 4loy | 6XS | Prothrombin | 3.4.21.5 | 0.546 | |
| 1ta2 | 176 | Prothrombin | 3.4.21.5 | 0.545 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.545 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.543 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.542 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.538 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.537 | |
| 2gde | SN3 | Prothrombin | 3.4.21.5 | 0.534 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.533 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.531 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.529 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.524 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.524 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.524 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.523 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.519 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.519 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.492 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.489 | |
| 4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.488 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.485 | |
| 1zsk | 421 | Coagulation factor XI | 3.4.21.27 | 0.484 | |
| 3v2u | ATP | Protein GAL3 | / | 0.475 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.475 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.474 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.474 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.474 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.474 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.472 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.471 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.471 | |
| 1owe | 675 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.471 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.471 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.471 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.470 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.469 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.468 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.466 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.466 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 1fml | RTL | Retinol dehydratase | / | 0.465 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.465 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.463 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.461 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.461 | |
| 1sqt | UI3 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.460 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.460 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 4b1j | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.459 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.458 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.457 | |
| 1sl3 | 170 | Prothrombin | 3.4.21.5 | 0.457 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.456 | |
| 1aa6 | MGD | Formate dehydrogenase H | 1.1.99.33 | 0.455 | |
| 3c36 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.455 | |
| 3hii | PNT | Amiloride-sensitive amine oxidase [copper-containing] | / | 0.455 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.455 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 2viv | VG2 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.454 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 1h66 | RH1 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.452 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.452 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.451 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.451 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.451 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.450 | |
| 3ab1 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.450 | |
| 3elb | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.449 | |
| 4brd | ANP | Ectonucleoside triphosphate diphosphohydrolase I | / | 0.449 | |
| 4fuf | 8UP | Urokinase-type plasminogen activator | 3.4.21.73 | 0.449 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.449 | |
| 5fd8 | A5A | Putative carboxypeptidase yocD | / | 0.449 | |
| 1ndh | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.448 | |
| 3iqi | ASN_GLU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.448 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.448 | |
| 1c1u | BAI | Prothrombin | 3.4.21.5 | 0.447 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.447 | |
| 2aq8 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.447 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.447 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.447 | |
| 4fue | 7UP | Urokinase-type plasminogen activator | 3.4.21.73 | 0.447 | |
| 1wli | FMN | FMN-binding protein | / | 0.446 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 2po3 | T4K | 4-dehydrase | / | 0.446 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.446 | |
| 1jqd | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.445 | |
| 1ptj | NAP | NAD(P) transhydrogenase subunit beta | 1.6.1.2 | 0.445 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.445 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.445 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.444 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2aot | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.444 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.444 | |
| 4f7i | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.444 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.443 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.443 | |
| 4x7z | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.443 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 1xh8 | R55 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 2hxz | H7J | Cathepsin S | 3.4.22.27 | 0.442 | |
| 2nq8 | ZID | Enoyl-ACP reductase | / | 0.442 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.442 | |
| 4dld | TZG | Glutamate receptor ionotropic, kainate 1 | / | 0.442 | |
| 4n82 | FMN | Ribonucleotide reductase (NrdI family protein), putative | / | 0.442 | |
| 1mcz | RMN | Benzoylformate decarboxylase | 4.1.1.7 | 0.441 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.441 | |
| 1zdw | FLV | Prenyltransferase | / | 0.441 | |
| 2nr4 | FMN | Conserved protein | / | 0.441 | |
| 2rfi | SAH | Histone-lysine N-methyltransferase EHMT1 | / | 0.441 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.441 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.441 | |
| 3fr2 | 8CA | Fatty acid-binding protein, adipocyte | / | 0.441 | |
| 3gf4 | U5P | UDP-galactopyranose mutase | 5.4.99.9 | 0.441 | |
| 4b1e | 6T6 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4na4 | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.441 | |
| 4usq | FAD | Pyridine nucleotide-disulfide oxidoreductase | / | 0.441 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.440 | |
| 1xvv | CCQ | L-carnitine CoA-transferase | / | 0.440 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.440 | |
| 3zvm | ADP | Bifunctional polynucleotide phosphatase/kinase | 2.7.1.78 | 0.440 | |
| 4b68 | NAP | L-ornithine N(5)-monooxygenase | / | 0.440 | |
| 4gyz | D5M | Tyrosyl-DNA phosphodiesterase 2 | 3.1.4 | 0.440 |