scPDB - Distribution of Cavity Similarity values of 3m8p 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
3m8p	65B	Gag-Pol polyprotein	2.7.7.49

Complex with similar cavities

PDB ID	HET	Uniprot Name	EC Number	Cavity Similarity
3m8p	65B	Gag-Pol polyprotein	2.7.7.49	1.000
3mec	65B	Gag-Pol polyprotein	2.7.7.49	0.633
3nbp	JGZ	Gag-Pol polyprotein	2.7.7.49	0.610
3m8q	DJZ	Gag-Pol polyprotein	2.7.7.49	0.604
3med	65B	Gag-Pol polyprotein	2.7.7.49	0.594
2ze2	T27	Gag-Pol polyprotein	2.7.7.49	0.553
4i2q	1BT	Gag-Pol polyprotein	2.7.7.49	0.535
3qlh	T27	Gag-Pol polyprotein	2.7.7.49	0.531
4i2p	G73	Gag-Pol polyprotein	2.7.7.49	0.531
3is9	AC7	Gag-Pol polyprotein	2.7.7.49	0.525
4g1q	T27	Gag-Pol polyprotein	2.7.7.49	0.521
4id5	T27	Gag-Pol polyprotein	2.7.7.49	0.512
3i0r	RT3	Gag-Pol polyprotein	2.7.7.49	0.510
3mee	T27	Gag-Pol polyprotein	2.7.7.49	0.510
2zd1	T27	Gag-Pol polyprotein	2.7.7.49	0.508
3meg	T27	Gag-Pol polyprotein	2.7.7.49	0.507
4rw6	494	Gag-Pol polyprotein	2.7.7.49	0.507
1c1b	GCA	Gag-Pol polyprotein	2.7.7.49	0.504
3i0s	RT7	Gag-Pol polyprotein	2.7.7.49	0.501
1tl3	H20	Gag-Pol polyprotein	2.7.7.49	0.499
1eet	BFU	Gag-Pol polyprotein	2.7.7.49	0.498
1jlc	FTC	Gag-Pol polyprotein	2.7.7.49	0.496
1tkt	H12	Gag-Pol polyprotein	2.7.7.49	0.496
3lan	KBT	Gag-Pol polyprotein	2.7.7.49	0.494
1iky	MSD	Gag-Pol polyprotein	2.7.7.49	0.493
3irx	UDR	Gag-Pol polyprotein	2.7.7.49	0.493
1s9e	ADB	Gag-Pol polyprotein	2.7.7.49	0.489
1tl1	H18	Gag-Pol polyprotein	2.7.7.49	0.488
1ikw	EFZ	Gag-Pol polyprotein	2.7.7.49	0.487
3bgr	T27	Gag-Pol polyprotein	2.7.7.49	0.486
1rt7	UC4	Gag-Pol polyprotein	2.7.7.49	0.485
1s6q	TPB	Gag-Pol polyprotein	2.7.7.49	0.485
4ifv	T27	Gag-Pol polyprotein	2.7.7.49	0.480
2rf2	MRX	Gag-Pol polyprotein	2.7.7.49	0.479
1hpz	AAP	Gag-Pol polyprotein	2.7.7.49	0.478
2ops	HBQ	Gag-Pol polyprotein	2.7.7.49	0.476
3c6u	M22	Gag-Pol polyprotein	2.7.7.49	0.476
2chz	093	Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform	2.7.1.153	0.475
3ffi	3OB	Gag-Pol polyprotein	2.7.7.49	0.474
3nx4	NAP	Putative oxidoreductase	/	0.474
1rt4	UC1	Gag-Pol polyprotein	2.7.7.49	0.473
1fk9	EFZ	Gag-Pol polyprotein	2.7.7.49	0.472
2prh	238	Dihydroorotate dehydrogenase (quinone), mitochondrial	1.3.5.2	0.472
3lal	KRV	Gag-Pol polyprotein	2.7.7.49	0.468
1hni	AAA	Gag-Pol polyprotein	2.7.7.49	0.467
1klm	SPP	Gag-Pol polyprotein	2.7.7.49	0.467
4kfb	T27	Gag-Pol polyprotein	2.7.7.49	0.467
1i7i	AZ2	Peroxisome proliferator-activated receptor gamma	/	0.466
3dle	GFA	Gag-Pol polyprotein	2.7.7.49	0.466
4ele	31I	Dihydrofolate reductase	/	0.466
1hnv	TBO	Gag-Pol polyprotein	2.7.7.49	0.463
1uzw	CDH	Isopenicillin N synthase	1.21.3.1	0.463
1jpa	ANP	Ephrin type-B receptor 2	2.7.10.1	0.462
1rev	TB9	Gag-Pol polyprotein	2.7.7.49	0.462
1rt2	TNK	Gag-Pol polyprotein	2.7.7.49	0.462
1tvr	TB9	Gag-Pol polyprotein	2.7.7.49	0.462
4i7f	NVE	Gag-Pol polyprotein	2.7.7.49	0.462
3vt8	YI3	Vitamin D3 receptor	/	0.461
1rt5	UC2	Gag-Pol polyprotein	2.7.7.49	0.460
4kko	1RE	Gag-Pol polyprotein	2.7.7.49	0.460
1d3h	A26	Dihydroorotate dehydrogenase (quinone), mitochondrial	1.3.5.2	0.458
2p4y	C03	Peroxisome proliferator-activated receptor gamma	/	0.457
3fl8	RAR	Dihydrofolate reductase	/	0.457
3zky	WT4	Isopenicillin N synthase	1.21.3.1	0.457
4wo5	324	Serine/threonine-protein kinase B-raf	2.7.11.1	0.457
3dmj	GWE	Pol protein	/	0.456
3vqu	O22	Dual specificity protein kinase TTK	2.7.12.1	0.456
1c1c	612	Gag-Pol polyprotein	2.7.7.49	0.455
3ruk	AER	Steroid 17-alpha-hydroxylase/17,20 lyase	/	0.455
1oc1	ASV	Isopenicillin N synthase	1.21.3.1	0.454
1s1w	UC1	Gag-Pol polyprotein	2.7.7.49	0.454
2wuf	KEM	4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase	3.7.1.17	0.454
3sgt	P09	Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)	/	0.454
4ko0	JLJ	Gag-Pol polyprotein	2.7.7.49	0.454
2hdh	NAD	Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial	1.1.1.35	0.452
2vg7	NNI	Gag-Pol polyprotein	2.7.7.49	0.452
4ig3	T27	Gag-Pol polyprotein	2.7.7.49	0.451
1hb1	OCV	Isopenicillin N synthase	1.21.3.1	0.450
2w9s	TOP	Dihydrofolate reductase type 1 from Tn4003	1.5.1.3	0.450
4lsl	1YQ	Gag-Pol polyprotein	2.7.7.49	0.450
4nky	3QZ	Steroid 17-alpha-hydroxylase/17,20 lyase	/	0.450
3uzc	T4E	Adenosine receptor A2a	/	0.450
3h0a	D30	Peroxisome proliferator-activated receptor gamma	/	0.449
4jib	1L6	cGMP-dependent 3',5'-cyclic phosphodiesterase	3.1.4.17	0.449
2znn	S44	Peroxisome proliferator-activated receptor alpha	/	0.448
3h1j	SMA	Cytochrome b	/	0.448
3l8p	0CE	Angiopoietin-1 receptor	2.7.10.1	0.448
3mdm	FJZ	Cholesterol 24-hydroxylase	/	0.448
4em3	FAD	Coenzyme A disulfide reductase	/	0.448
4imo	PWZ	Prostaglandin-H2 D-isomerase	5.3.99.2	0.448
1ikv	EFZ	Gag-Pol polyprotein	2.7.7.49	0.447
2bu9	HFV	Isopenicillin N synthase	1.21.3.1	0.447
3lj3	WYE	Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform	2.7.1.153	0.447
3p6o	ETG	Camphor 5-monooxygenase	1.14.15.1	0.447
3slk	NDP	Polyketide synthase extender module 2	/	0.447
1d3g	BRE	Dihydroorotate dehydrogenase (quinone), mitochondrial	1.3.5.2	0.446
1ikx	PNU	Gag-Pol polyprotein	2.7.7.49	0.446
2y03	Y01	Beta-1 adrenergic receptor	/	0.446
3dok	GWJ	Pol protein	/	0.446
3fco	IIG	Corticosteroid 11-beta-dehydrogenase isozyme 1	1.1.1.146	0.446
3lam	KRP	Gag-Pol polyprotein	2.7.7.49	0.446
5cyq	T27	Gag-Pol polyprotein	2.7.7.49	0.446
5jla	NAD	Putative short-chain dehydrogenase/reductase	/	0.446
3rfm	CFF	Adenosine receptor A2a	/	0.446
1q5d	EPB	Epothilone C/D epoxidase	1.14	0.445
3s1d	ZIR	Cytokinin dehydrogenase 1	1.5.99.12	0.445
4o71	CPB	Bromodomain-containing protein 4	/	0.445
3rey	XAC	Adenosine receptor A2a	/	0.445
1lso	NAD	Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial	1.1.1.35	0.444
1osv	CHC	Bile acid receptor	/	0.444
3ics	ADP	Coenzyme A disulfide reductase	/	0.444
3vt5	YI2	Vitamin D3 receptor	/	0.444
3zoi	M2W	Isopenicillin N synthase	1.21.3.1	0.444
1rt1	MKC	Gag-Pol polyprotein	2.7.7.49	0.443
3eek	53S	Uncharacterized protein	/	0.443
4j03	FVS	Bifunctional epoxide hydrolase 2	3.1.3.76	0.443
3w0a	DS5	Vitamin D3 receptor	/	0.442
4fhh	0U3	Vitamin D3 receptor A	/	0.442
5k2b	ZMA	Adenosine receptor A2a	/	0.442
1jlg	UC1	Gag-Pol polyprotein	2.7.7.49	0.441
1o8c	NDP	Probable acrylyl-CoA reductase AcuI	1.3.1.84	0.441
1tw4	CHD	Fatty acid-binding protein, liver	/	0.441
2ivi	ACW	Isopenicillin N synthase	1.21.3.1	0.441
2vcm	M11	Isopenicillin N synthase	1.21.3.1	0.441
3dl9	V2H	Vitamin D 25-hydroxylase	/	0.441
3nc9	TR3	Ketohexokinase	/	0.441
3zw3	ZW3	Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform	2.7.1.153	0.441
4c58	824	Cyclin-G-associated kinase	2.7.11.1	0.441
4elb	34S	Dihydrofolate reductase	/	0.441
1vru	AAP	Gag-Pol polyprotein	2.7.7.49	0.440
4bid	IE8	Mitogen-activated protein kinase kinase kinase 5	2.7.11.25	0.440
4fjz	4FJ	Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform	2.7.1.153	0.440