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 |
|---|---|---|---|
| 3utu | 1TS | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 1.000 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.746 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.702 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.699 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.689 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.669 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.668 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.665 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.664 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.660 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.656 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.654 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.653 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.649 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.649 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.646 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.646 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.639 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.635 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.624 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.622 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.621 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.619 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.615 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.615 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.614 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.612 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.611 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.610 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.608 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.607 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.607 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.607 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.605 | |
| 1ypg | UIR | Prothrombin | 3.4.21.5 | 0.605 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.603 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.600 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.600 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.599 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.599 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.599 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.592 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.591 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.590 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.589 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.588 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.586 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.585 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.585 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.585 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.584 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.583 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.583 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.583 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.583 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.582 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.582 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.581 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.581 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.580 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.580 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.580 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.579 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.578 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.576 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.575 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.574 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.574 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.574 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.572 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.571 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.570 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.567 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.566 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.564 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.562 | |
| 2jh0 | 701 | Prothrombin | 3.4.21.5 | 0.560 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.559 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.555 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.554 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.552 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.551 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.550 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.549 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.546 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.546 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.545 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.543 | |
| 2cn0 | F25 | Prothrombin | 3.4.21.5 | 0.543 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.542 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.538 | |
| 2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.528 | |
| 2gde | SN3 | Prothrombin | 3.4.21.5 | 0.528 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.527 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.512 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.509 | |
| 4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.508 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.501 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.479 | |
| 1knr | FAD | L-aspartate oxidase | 1.4.3.16 | 0.478 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.478 | |
| 1qo8 | FAD | Fumarate reductase flavoprotein subunit | / | 0.477 | |
| 3sf6 | FDA | Glutaryl-CoA dehydrogenase | / | 0.476 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.475 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.472 | |
| 1c7o | PPG | Hemolysin | / | 0.471 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.471 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.470 | |
| 3k5g | BJC | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.469 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.467 | |
| 2b8l | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.467 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.467 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.466 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.465 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.465 | |
| 5eb5 | FAD | (R)-mandelonitrile lyase 1 | 4.1.2.10 | 0.464 | |
| 1zga | HMK | Isoflavone 4'-O-methyltransferase | / | 0.463 | |
| 2fhl | BNI | Avidin-related protein 4/5 | / | 0.463 | |
| 2vjm | COA | Formyl-CoA:oxalate CoA-transferase | / | 0.463 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.462 | |
| 2wf3 | ZY3 | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.459 | |
| 2wf1 | ZY1 | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 1eji | THF | Serine hydroxymethyltransferase, cytosolic | / | 0.457 | |
| 4yry | FAD | Glutamate synthase, beta subunit | / | 0.456 | |
| 2iya | ZIO | Oleandomycin glycosyltransferase | / | 0.455 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.455 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.454 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.454 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.454 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.453 | |
| 3qbh | QBH | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 1gal | FAD | Glucose oxidase | 1.1.3.4 | 0.452 | |
| 2vnn | CM7 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 2rm2 | W43 | Genome polyprotein | / | 0.451 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 2bf4 | FMN | NADPH--cytochrome P450 reductase | / | 0.450 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
| 3kr8 | XAV | Tankyrase-2 | 2.4.2.30 | 0.450 | |
| 4z28 | BTN | Hoefavidin | / | 0.450 | |
| 1so2 | 666 | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.449 | |
| 1y7l | ASN_LEU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.449 | |
| 2xvf | FAD | Putative flavin-containing monooxygenase | / | 0.449 | |
| 3fcj | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.449 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.449 | |
| 4d03 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.449 | |
| 5c3a | URM | Histo-blood group ABO system transferase | / | 0.449 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.448 | |
| 1zdw | FLV | Prenyltransferase | / | 0.447 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.447 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.447 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.447 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 2wf2 | ZY2 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.446 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.444 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2ooy | ATP | 5'-AMP-activated protein kinase subunit gamma | / | 0.444 | |
| 4k8s | 1QT | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2bn4 | FMN | NADPH--cytochrome P450 reductase | / | 0.443 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 5il2 | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.443 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.442 | |
| 2npi | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.442 | |
| 2vmy | FFO | Serine hydroxymethyltransferase | / | 0.442 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.442 | |
| 3ha5 | SFG | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.442 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3nu0 | 3TU | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3vqs | JT1 | Genome polyprotein | / | 0.442 | |
| 4ytn | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.442 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.441 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.441 | |
| 2pvj | P44 | Casein kinase II subunit alpha | 2.7.11.1 | 0.441 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.441 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.441 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.441 | |
| 3v94 | WYQ | Phosphodiesterase | / | 0.441 | |
| 2q15 | 3MR | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3mb7 | 14I | Casein kinase II subunit alpha | 2.7.11.1 | 0.440 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.440 |