scPDB - Distribution of Cavity Similarity values of 2ddo entry / Site 1

Distribution of Cavity similarities measured by Shaper

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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

Reference Protein Data Bank Entry :

PDB ID	HET	Uniprot Name	EC Number
2ddo	ATP	Pyridoxine/pyridoxal/pyridoxamine kinase

Complex with similar cavities

PDB ID	HET	Uniprot Name	EC Number	Cavity Similarity
2ddo	ATP	Pyridoxine/pyridoxal/pyridoxamine kinase	/	1.000
3ibq	ATP	Pyridoxal kinase	/	0.473
4nbt	NAD	3-oxoacyl-[acyl-carrier-protein] reductase	/	0.473
3keu	ATP	Pyridoxal kinase	2.7.1.35	0.470
2chx	090	Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform	2.7.1.153	0.468
4c7k	NAP	Corticosteroid 11-beta-dehydrogenase isozyme 1	1.1.1.146	0.466
3drc	MTX	Dihydrofolate reductase	1.5.1.3	0.465
4cvm	ANP	UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase	/	0.463
2y60	M8F	Isopenicillin N synthase	1.21.3.1	0.462
1rfv	ADP	Pyridoxal kinase	2.7.1.35	0.461
2zba	ZBA	Trichothecene 3-O-acetyltransferase	/	0.461
1qjf	ACS	Isopenicillin N synthase	1.21.3.1	0.459
1xdd	AAY	Integrin alpha-L	/	0.458
2v16	C47	Renin	3.4.23.15	0.457
1kvs	UPG	UDP-glucose 4-epimerase	5.1.3.2	0.456
3lqf	NAD	Galactitol dehydrogenase	/	0.454
2gjn	FMN	Nitronate monooxygenase	1.13.12.16	0.453
2vbd	V10	Isopenicillin N synthase	1.21.3.1	0.453
3qt6	2P0	Mevalonate diphosphate decarboxylase	/	0.453
2chz	093	Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform	2.7.1.153	0.452
2bu9	HFV	Isopenicillin N synthase	1.21.3.1	0.451
2cf6	NAP	Cinnamyl alcohol dehydrogenase 5	1.1.1.195	0.451
2jb4	A14	Isopenicillin N synthase	1.21.3.1	0.451
2y6f	M9F	Isopenicillin N synthase	1.21.3.1	0.451
4nbw	NAD	Short-chain dehydrogenase/reductase SDR	/	0.450
2ktd	PUC	Prostaglandin-H2 D-isomerase	5.3.99.2	0.449
4k28	NAD	Shikimate dehydrogenase family protein	/	0.449
1rfu	ADP	Pyridoxal kinase	2.7.1.35	0.448
2vbp	VB1	Isopenicillin N synthase	1.21.3.1	0.448
2gjl	FMN	Nitronate monooxygenase	1.13.12.16	0.447
2rhr	EMO	Putative ketoacyl reductase	1.3.1	0.447
4a81	DXC	Major pollen allergen Bet v 1-A	/	0.447
1rne	C60	Renin	3.4.23.15	0.446
2bri	ANP	Uridylate kinase	2.7.4.22	0.446
2y0m	ACO	Histone acetyltransferase KAT8	/	0.446
4fri	DWA	Beta-secretase 1	3.4.23.46	0.446
1bvr	NAD	Enoyl-[acyl-carrier-protein] reductase [NADH]	1.3.1.9	0.445
2fr0	NDP	6-deoxyerythronolide-B synthase EryA1, modules 1 and 2	/	0.445
3zoi	M2W	Isopenicillin N synthase	1.21.3.1	0.445
4j0v	1H7	Beta-secretase 1	3.4.23.46	0.445
1e6w	NAD	3-hydroxyacyl-CoA dehydrogenase type-2	1.1.1.35	0.444
1qiq	ACC	Isopenicillin N synthase	1.21.3.1	0.444
4l4e	CAM	Camphor 5-monooxygenase	1.14.15.1	0.444
1hb1	OCV	Isopenicillin N synthase	1.21.3.1	0.443
3tk3	CPZ	Cytochrome P450 2B4	1.14.14.1	0.443
4bge	PYW	Enoyl-[acyl-carrier-protein] reductase [NADH]	1.3.1.9	0.443
1oc1	ASV	Isopenicillin N synthase	1.21.3.1	0.442
1xe5	5FE	Plasmepsin-2	3.4.23.39	0.442
3oad	LPO	Renin	3.4.23.15	0.442
4gj3	0XP	Non-receptor tyrosine-protein kinase TYK2	2.7.10.2	0.442
1o9b	NAI	Quinate/shikimate dehydrogenase	/	0.441
3dy8	IBM	High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A	/	0.441
4f4d	CHD	Ferrochelatase, mitochondrial	4.99.1.1	0.441
3oey	NAD	Enoyl-[acyl-carrier-protein] reductase [NADH]	1.3.1.9	0.440
4bii	PYW	Enoyl-[acyl-carrier-protein] reductase [NADH]	1.3.1.9	0.440