3DDU.A | PREP – ASTRID

3DDU.A | PREP

General Structure Information

PDB ID	3ddu
HGNC Gene Label(s)	PREP
Structure Name	prolyl oligopeptidase with gsk552
Resolution	1.56Å
Reference	AUTH C.D.HAFFNER,C.J.DIAZ,A.B.MILLER,R.A.REID,K.P.MADAUSS,AUTH 2 A.HASSELL,M.H.HANLON,D.J.PORTER,J.D.BECHERER,L.H.CARTERTITL PYRROLIDINYL PYRIDONE AND PYRAZINONE ANALOGUES AS POTENTTITL 2 INHIBITORS OF PROLYL OLIGOPEPTIDASE (POP)REF BIOORG.MED.CHEM.LETT. V. 18 4360 2008REFN ISSN 0960-894XPMID 18606544DOI 10.1016/J.BMCL.2008.06.067

Variant Set Distributions

ExAC Variants

Number Of Residues	707
Number Of SNVs	149
Number Of Permutations	60523
Optimal Distance Threshold	22.0
K Statistic	0.186
p-value	0.132

COSMIC

Number Of Residues	707
Number Of SNVs	5
Number Of Permutations	454
Optimal Distance Threshold	29.0
K Statistic	0.2
p-value	0.53

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	149
Number Of COSMIC SNVs	5
Optimal Distance Threshold	22.0
K Statistic	-0.186
p-value	0.334

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
6:105850759	rs201961022	S>C	A:3	(12.21, -7.36, 3.59)
6:105845802		V>I	A:16	(-11.90, 17.97, 2.17)
6:105845795		D>G	A:18	(-13.04, 24.34, 5.84)
6:105845763		A>T	A:29	(-10.66, 9.10, 7.19)
6:105845745	COSM1071730	D>N	A:35	(-15.95, -1.58, 13.32)
6:105845729		K>T	A:40	(-10.87, -4.93, 10.68)
6:105825394		A>T	A:41	(-7.43, -5.11, 6.48)
6:105825382		A>S	A:45	(-1.38, -5.96, 6.67)
6:105825371		K>N	A:48	(0.56, -10.21, 8.07)
6:105825364	COSM739799	V>L	A:51	(5.67, -9.53, 13.27)
6:105825340		I>V	A:59	(18.78, -9.06, 19.24)
6:105825297		Y>C	A:73	(12.06, -7.58, 40.65)
6:105825280	rs145437152	H>Y	A:79	(2.15, -2.78, 54.04)
6:105825267	rs143212777	G>A	A:83	(-8.89, -0.85, 60.14)
6:105825261	rs372844544	R>Q	A:85	(-8.45, -6.19, 58.71)
6:105824128	rs192851228	Y>C	A:86	(-1.85, -3.54, 58.48)
6:105824120		F>I	A:89	(-1.25, -4.34, 46.06)
6:105824092		R>Q	A:98	(0.06, -5.23, 42.05)
6:105824084		Y>H	A:101	(-1.42, -10.60, 49.28)
6:105824051		V>M	A:112	(-5.13, -13.97, 48.93)
6:105824031		I>M	A:118	(-8.44, -15.83, 38.95)
6:105824033		I>V	A:118	(-8.44, -15.83, 38.95)
6:105824002	COSM1642820	R>Q	A:128	(-8.71, 1.21, 35.94)
6:105821447		A>V	A:131	(-12.58, 1.78, 48.06)
6:105821441		S>N	A:133	(-14.98, 1.30, 54.26)
6:105821439	rs545041244	E>K	A:134	(-13.85, 5.05, 57.49)
6:105821436	rs373499166	D>N	A:135	(-15.26, 0.20, 58.83)
6:105821429		E>V	A:137	(-15.13, -4.31, 57.75)
6:105821426		Y>C	A:138	(-18.17, -3.98, 53.85)
6:105821417		Y>C	A:141	(-13.53, -4.75, 43.05)
6:105821402	rs376236808	S>N	A:146	(-8.56, -5.26, 27.35)
6:105821373		M>V	A:156	(-15.38, -7.71, 48.64)
6:105821370		K>E	A:157	(-17.78, -9.09, 53.93)
6:105821361		G>R	A:160	(-13.84, -13.55, 53.93)
6:105821345		P>L	A:165	(-24.37, -8.68, 44.95)
6:105821346	rs372805012	P>S	A:165	(-24.37, -8.68, 44.95)
6:105821341		D>E	A:166	(-23.34, -4.85, 44.81)
6:105821328		V>L	A:171	(-17.76, 3.38, 35.44)
6:105821324		K>R	A:172	(-14.96, 6.27, 31.87)
6:105821303		T>S	A:179	(-20.56, 7.47, 53.28)
6:105821300		H>R	A:180	(-17.29, 8.17, 56.91)
6:105821286	rs148932244	M>V	A:185	(-19.72, 4.37, 46.89)
6:105821282	rs369321437	F>Y	A:186	(-20.58, 9.39, 46.63)
6:105821273		S>L	A:189	(-21.73, 7.61, 35.33)
6:105821258	rs573925864	D>G	A:194	(-25.96, 4.27, 20.54)
6:105821249		S>N	A:197	(-18.99, 0.51, 25.71)
6:105816887		S>Y	A:203	(-17.57, 7.47, 21.30)
6:105816881	rs546242317	N>S	A:205	(-16.83, 10.36, 26.74)
6:105816857		H>R	A:213	(-24.70, 1.89, 45.39)
6:105816845	rs369220661	T>S	A:217	(-29.05, -1.71, 46.09)
6:105816843	rs145682559	D>N	A:218	(-30.34, -2.84, 42.20)
6:105816827		I>N	A:223	(-29.26, 8.69, 44.42)
6:105816818		A>V	A:226	(-24.47, 15.69, 40.39)
6:105816810	rs202011848	P>T	A:229	(-26.95, 19.89, 32.16)
6:105816788		G>A	A:236	(-17.58, 15.29, 39.44)
6:105800936	COSM1071726	R>H	A:245	(-20.23, 17.86, 58.97)
6:105800937	rs149858250	R>C	A:245	(-20.23, 17.86, 58.97)
6:105800916		R>G	A:252	(-11.36, 18.68, 37.70)
6:105800849	rs201202923	A>V	A:274	(-32.24, 11.80, 48.06)
6:105800850		A>T	A:274	(-32.24, 11.80, 48.06)
6:105800847		G>R	A:275	(-30.48, 13.83, 45.75)
6:105781350		N>S	A:285	(-13.76, 29.52, 39.80)
6:105781329		Y>C	A:292	(-9.40, 17.46, 51.98)
6:105781326	rs200495985	V>A	A:293	(-5.33, 17.80, 53.11)
6:105781320	rs139598379	N>S	A:295	(-11.13, 19.03, 58.37)
6:105781311	rs535207006 COSM3154187	T>M	A:298	(-14.93, 25.10, 59.68)
6:105781304		F>L	A:300	(-11.81, 22.51, 55.27)
6:105781293		T>R	A:304	(-3.15, 25.79, 45.97)
6:105781274		N>K	A:310	(5.91, 26.27, 42.61)
6:105781275	rs374389008	N>S	A:310	(5.91, 26.27, 42.61)
6:105781272		Y>C	A:311	(1.32, 23.86, 43.24)
6:105781269	rs371261992	R>H	A:312	(0.11, 28.63, 48.54)
6:105781267	rs144257084	V>M	A:313	(-0.66, 24.87, 52.04)
6:105781264		I>V	A:314	(-4.54, 27.21, 51.64)
6:105781233		S>F	A:324	(-8.92, 38.06, 52.23)
6:105781224	rs529312341	K>R	A:327	(-5.02, 32.05, 57.03)
6:105776880		S>Y	A:346	(-4.06, 13.86, 63.78)
6:105776866	rs12192054	L>V	A:351	(5.10, 17.87, 52.69)
6:105776848		V>I	A:357	(13.71, 16.34, 38.64)
6:105776827		H>Y	A:364	(5.79, 20.12, 57.78)
6:105776808		A>V	A:370	(6.43, 23.69, 60.71)
6:105776809	rs369849841	A>T	A:370	(6.43, 23.69, 60.71)
6:105776798		K>N	A:373	(12.06, 14.67, 60.30)
6:105776796	rs149545819	T>S	A:374	(14.20, 15.95, 56.69)
6:105776794		F>L	A:375	(11.27, 11.76, 56.21)
6:105776790	rs372127457	P>L	A:376	(16.32, 10.57, 54.59)
6:105776785	rs147546055	D>N	A:378	(19.01, 8.26, 47.91)
6:105776779	rs548769535	G>S	A:380	(14.60, 10.14, 43.18)
6:105776758		G>S	A:387	(-1.25, 7.84, 55.64)
6:105776749		K>E	A:390	(-7.41, 7.11, 61.40)
6:105776743		T>P	A:392	(0.11, 5.98, 63.91)
6:105771640		I>S	A:406	(12.80, 0.87, 49.11)
6:105771634	rs539227032	Y>C	A:408	(12.17, 3.56, 53.16)
6:105771620		T>A	A:413	(4.08, 7.20, 68.05)
6:105771592		F>S	A:422	(8.80, -2.87, 55.91)
6:105771589	rs141737006	R>Q	A:423	(10.31, -5.88, 51.78)
6:105771578	rs551134826	V>I	A:427	(18.24, -7.25, 40.49)
6:105771566	rs147656266	D>N	A:431	(26.76, -3.41, 40.00)
6:105771560		S>A	A:433	(28.84, 0.33, 40.74)
6:105771544		V>A	A:438	(24.47, 12.59, 35.06)
6:105736765		F>S	A:441	(20.78, 21.68, 33.93)
6:105736754		K>E	A:445	(15.37, 28.15, 19.71)
6:105736744	rs148175713	T>M	A:448	(15.40, 27.92, 28.53)
6:105736733	rs145698846	M>V	A:452	(19.25, 15.76, 30.27)
6:105736727	rs531198200	I>V	A:454	(22.71, 11.18, 31.13)
6:105736693		S>C	A:465	(30.13, 5.29, 19.44)
6:105736676		Y>H	A:471	(11.06, 9.22, 27.67)
6:105736673	rs377361545	G>S	A:472	(9.83, 12.06, 26.40)
6:105736652	rs148303604	S>P	A:479	(6.97, 15.14, 36.15)
6:105736636		Y>C	A:484	(14.78, -0.40, 38.31)
6:105733427		M>V	A:495	(22.26, -3.03, 23.12)
6:105733416	COSM3920555	I>M	A:498	(22.75, 5.56, 26.28)
6:105733408		V>A	A:501	(15.31, 11.85, 30.49)
6:105733402		N>S	A:503	(12.99, 17.14, 32.08)
6:105733400		I>V	A:504	(10.58, 18.84, 27.87)
6:105733372	COSM170059	T>M	A:513	(5.82, 28.27, 34.79)
6:105733366		H>R	A:515	(1.89, 23.21, 31.92)
6:105733362		K>N	A:516	(1.54, 27.94, 31.54)
6:105730452		I>V	A:519	(0.70, 25.06, 26.75)
6:105730406		A>V	A:534	(19.76, 15.68, 20.67)
6:105730404		E>K	A:535	(21.24, 19.41, 18.99)
6:105730394	rs201312087	I>T	A:538	(25.14, 14.74, 18.94)
6:105730392		K>Q	A:539	(28.65, 19.03, 21.34)
6:105730374	COSM3619161	P>S	A:545	(22.70, 11.17, 14.40)
6:105729753		D>G	A:569	(18.61, 15.40, 10.60)
6:105729663		Y>C	A:599	(-2.71, 19.58, 22.83)
6:105729655		S>A	A:602	(-9.59, 22.99, 15.39)
6:105729650		D>E	A:603	(-13.31, 24.17, 16.55)
6:105729652		D>N	A:603	(-13.31, 24.17, 16.55)
6:105729645		K>R	A:605	(-8.63, 31.14, 12.83)
6:105729641		Q>H	A:606	(-5.91, 31.50, 17.95)
6:105726294		V>M	A:620	(4.40, 13.97, 6.29)
6:105726242	rs149696511	T>S	A:637	(-1.36, 0.81, 19.11)
6:105726224		R>H	A:643	(-6.85, 7.64, 27.72)
6:105726225		R>C	A:643	(-6.85, 7.64, 27.72)
6:105726213	rs150938968	L>F	A:647	(-7.59, 6.89, 14.56)
6:105726189		T>A	A:655	(0.71, 9.33, 5.59)
6:105726177		I>V	A:659	(4.41, 10.81, 1.30)
6:105726167	COSM200448	R>H	A:662	(5.56, 6.67, -2.84)
6:105726168	COSM3697429	R>C	A:662	(5.56, 6.67, -2.84)
6:105726164	rs377611251	S>N	A:663	(10.93, 7.33, -1.52)
6:105726141	rs375975022	L>I	A:671	(6.74, -0.36, 10.70)
6:105726134		H>R	A:673	(1.95, -4.11, 16.54)
6:105726132	rs200608024	V>M	A:674	(-2.13, -3.20, 16.36)
6:105726122	COSM297070	K>R	A:677	(-6.99, -8.77, 24.90)
6:105726119		A>V	A:678	(-4.82, -3.78, 24.73)
6:105726107	rs201327468	A>V	A:682	(-3.04, 0.65, 32.16)
6:105726108		A>T	A:682	(-3.04, 0.65, 32.16)
6:105726099		P>A	A:685	(-0.21, -7.70, 31.04)
6:105726079		E>D	A:691	(6.51, -9.67, 24.08)
6:105726069	rs146276553	D>Y	A:695	(8.89, -5.64, 19.93)
6:105726065		M>T	A:696	(10.83, -1.18, 21.82)
6:105726059		A>V	A:698	(14.44, -5.24, 18.05)
6:105726054		I>V	A:700	(16.67, -0.17, 18.25)
6:105726051	COSM396159	A>T	A:701	(18.81, -3.65, 16.61)
6:105726047	rs139931686	R>Q	A:702	(16.39, -5.52, 11.43)
6:105726048	rs368281704	R>W	A:702	(16.39, -5.52, 11.43)
6:105726035		V>A	A:706	(22.95, -3.14, 17.63)
6:105726036	rs1051484	V>I	A:706	(22.95, -3.14, 17.63)
6:105726033	rs554298353	D>N	A:707	(26.10, -6.35, 18.15)
6:105726024		P>A	A:710	(27.33, -11.04, 26.28)

3DDU.A | PREP.

3DDU.A | PREP

General Structure Information

Variant Set Distributions

Ripley’s K Analysis Plots

Variant Set Comparisons

Mapped Variants

[+] ExAC Missense Variants

[+] COSMIC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
6:105800946	COSM2157153	D>N	A:242	(-10.93, 13.15, 57.28)
6:105800891	COSM1071725	R>Q	A:260	(-16.15, 25.33, 39.47)
6:105771589	COSM2156564	R>Q	A:423	(10.31, -5.88, 51.78)
6:105726216	COSM253811	P>S	A:646	(-6.25, 3.65, 17.44)
6:105726167	COSM200448	R>H	A:662	(5.56, 6.67, -2.84)