General Structure Information
| PDB ID | 1z10 |
| HGNC Gene Label(s) | CYP2A6 |
| Structure Name | crystal structure of human microsomal p450 2a6 with coumarin bound |
| Resolution | 1.9Å |
| Reference | AUTH J.K.YANO,M.H.HSU,K.J.GRIFFIN,C.D.STOUT,E.F.JOHNSONTITL STRUCTURES OF HUMAN MICROSOMAL CYTOCHROME P450 2A6 COMPLEXEDTITL 2 WITH COUMARIN AND METHOXSALENREF NAT.STRUCT.MOL.BIOL. V. 12 822 2005REFN ISSN 1545-9993PMID 16086027DOI 10.1038/NSMB971 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 464 |
| Number Of SNVs | 133 |
| Number Of Permutations | 25162 |
| Optimal Distance Threshold | 6.0 |
| K Statistic | 0.011 |
| p-value | 0.626 |
COSMIC
| Number Of Residues | 464 |
| Number Of SNVs | 13 |
| Number Of Permutations | 3701 |
| Optimal Distance Threshold | 18.0 |
| K Statistic | 0.295 |
| p-value | 0.132 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 133 |
| Number Of COSMIC SNVs | 10 |
| Optimal Distance Threshold | 17.0 |
| K Statistic | 0.153 |
| p-value | 0.11 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 19:41356228 | rs377713545 | P>R | D:35 | (81.14, 57.42, 82.86) |
| 19:41356223 | P>A | D:37 | (74.53, 53.96, 83.93) | |
| 19:41356213 | L>W | D:40 | (65.80, 53.31, 79.32) | |
| 19:41356210 | P>L | D:41 | (63.98, 55.91, 76.87) | |
| 19:41356204 | rs575050301 | I>T | D:43 | (62.78, 55.97, 82.62) |
| 19:41356205 | I>L | D:43 | (62.78, 55.97, 82.62) | |
| 19:41356201 | rs144279119 | G>A | D:44 | (66.38, 56.65, 82.56) |
| 19:41356183 | rs374253823 | N>S | D:50 | (65.91, 53.89, 95.79) |
| 19:41356171 | M>K | D:54 | (68.77, 59.18, 95.27) | |
| 19:41356162 | S>F | D:57 | (71.70, 54.86, 94.71) | |
| 19:41356159 | L>P | D:58 | (73.95, 58.23, 93.21) | |
| 19:41355884 | I>N | D:61 | (76.21, 54.29, 90.51) | |
| 19:41355885 | rs200554095 | I>F | D:61 | (76.21, 54.29, 90.51) |
| 19:41355875 | rs374515279 COSM996850 |
R>H | D:64 | (79.95, 49.19, 88.86) |
| 19:41355867 | P>S | D:67 | (84.28, 59.83, 90.96) | |
| 19:41355863 | V>A | D:68 | (82.94, 61.64, 87.70) | |
| 19:41355864 | rs143690364 | V>M | D:68 | (82.94, 61.64, 87.70) |
| 19:41355837 | R>W | D:77 | (72.50, 64.72, 80.20) | |
| 19:41355834 | V>I | D:78 | (73.04, 64.76, 86.03) | |
| 19:41355831 | COSM996849 | V>M | D:79 | (77.37, 65.32, 86.15) |
| 19:41355807 | rs143067113 | V>I | D:87 | (83.56, 68.50, 94.71) |
| 19:41355777 | rs145308399 | E>K | D:97 | (83.80, 76.42, 84.03) |
| 19:41355752 | A>V | D:105 | (61.50, 70.87, 90.96) | |
| 19:41355744 | D>N | D:108 | (61.81, 75.42, 90.44) | |
| 19:41355738 | rs72549435 | V>L | D:110 | (57.38, 78.86, 93.64) |
| 19:41355733 | F>L | D:111 | (61.18, 80.04, 93.91) | |
| 19:41355729 | G>S | D:113 | (63.88, 81.67, 88.41) | |
| 19:41354666 | rs376782364 COSM996848 |
V>M | D:116 | (69.06, 84.60, 95.06) |
| 19:41354662 | COSM3960099 | V>A | D:117 | (68.59, 80.48, 95.19) |
| 19:41354658 | F>L | D:118 | (66.58, 78.32, 92.74) | |
| 19:41354659 | F>Y | D:118 | (66.58, 78.32, 92.74) | |
| 19:41354660 | rs28399440 | F>L | D:118 | (66.58, 78.32, 92.74) |
| 19:41354657 | S>R | D:119 | (69.09, 82.72, 89.86) | |
| 19:41354650 | G>E | D:121 | (73.20, 85.18, 85.78) | |
| 19:41354651 | rs61562160 | G>R | D:121 | (73.20, 85.18, 85.78) |
| 19:41354648 | E>K | D:122 | (72.96, 90.04, 85.60) | |
| 19:41354639 | rs373566142 | K>Q | D:125 | (76.17, 89.19, 89.07) |
| 19:41354633 | L>F | D:127 | (69.60, 89.22, 93.32) | |
| 19:41354630 | R>W | D:128 | (75.43, 86.06, 95.92) | |
| 19:41354626 | rs554865113 | R>P | D:129 | (76.32, 92.63, 93.85) |
| 19:41354621 | rs59552350 | S>A | D:131 | (71.62, 90.00, 99.39) |
| 19:41354593 | V>A | D:140 | (75.52, 89.38, 109.12) | |
| 19:41354584 | R>P | D:143 | (78.62, 93.67, 119.53) | |
| 19:41354582 | G>S | D:144 | (73.98, 92.99, 116.30) | |
| 19:41354574 | E>D | D:146 | (76.37, 88.51, 118.80) | |
| 19:41354575 | E>G | D:146 | (76.37, 88.51, 118.80) | |
| 19:41354555 | rs2545783 | A>S | D:153 | (68.51, 82.48, 123.25) |
| 19:41354551 | G>D | D:154 | (66.63, 83.56, 125.86) | |
| 19:41354540 | D>N | D:158 | (62.68, 81.70, 128.96) | |
| 19:41354533 | rs1801272 | L>H | D:160 | (63.15, 75.20, 127.04) |
| 19:41354534 | rs60563539 | L>I | D:160 | (63.15, 75.20, 127.04) |
| 19:41354530 | R>P | D:161 | (64.06, 77.62, 132.27) | |
| 19:41354531 | R>W | D:161 | (64.06, 77.62, 132.27) | |
| 19:41354527 | G>D | D:162 | (58.31, 76.16, 130.82) | |
| 19:41354522 | G>S | D:164 | (59.42, 71.60, 133.19) | |
| 19:41354278 | N>S | D:167 | (58.73, 64.28, 126.95) | |
| 19:41354275 | I>N | D:168 | (59.04, 68.09, 124.61) | |
| 19:41354271 | rs150091942 | D>E | D:169 | (58.69, 67.80, 119.74) |
| 19:41354234 | I>L | D:182 | (66.13, 85.62, 109.03) | |
| 19:41354209 | rs571335587 | R>L | D:190 | (60.35, 88.38, 118.00) |
| 19:41354210 | R>S | D:190 | (60.35, 88.38, 118.00) | |
| 19:41354198 | rs199916117 COSM1129845 CM102862 |
K>E | D:194 | (51.72, 82.75, 122.41) |
| 19:41354187 | rs368174755 | E>D | D:197 | (50.57, 83.41, 110.78) |
| 19:41354188 | E>G | D:197 | (50.57, 83.41, 110.78) | |
| 19:41354185 | F>C | D:198 | (56.04, 81.89, 113.61) | |
| 19:41354182 | rs538011777 | L>P | D:199 | (53.17, 77.24, 114.00) |
| 19:41354172 | L>F | D:202 | (57.50, 77.07, 111.19) | |
| 19:41354170 | rs145393137 | R>H | D:203 | (53.38, 72.95, 111.31) |
| 19:41354152 | rs527966463 | F>C | D:209 | (63.46, 70.96, 103.91) |
| 19:41354143 | rs185545560 | T>M | D:212 | (62.10, 67.35, 99.22) |
| 19:41354138 | rs370474607 | T>A | D:214 | (60.29, 61.83, 100.18) |
| 19:41354134 | S>F | D:215 | (60.32, 58.72, 97.34) | |
| 19:41354126 | Q>E | D:218 | (63.90, 62.70, 94.92) | |
| 19:41352941 | rs111033610 | S>P | D:224 | (58.05, 67.24, 86.94) |
| 19:41352908 | Q>K | D:235 | (49.66, 68.85, 94.36) | |
| 19:41352884 | rs145148721 | G>R | D:243 | (51.80, 80.13, 101.57) |
| 19:41352875 | rs149223328 | D>Y | D:246 | (50.57, 84.04, 99.80) |
| 19:41352872 | F>L | D:247 | (53.69, 85.84, 105.19) | |
| 19:41352858 | rs374784083 COSM996844 |
K>N | D:251 | (54.82, 91.21, 105.54) |
| 19:41352845 | rs533216061 | Q>K | D:256 | (54.90, 98.89, 99.62) |
| 19:41352826 | N>S | D:262 | (65.20, 108.50, 103.83) | |
| 19:41352824 | COSM4078382 | S>T | D:263 | (64.80, 104.73, 107.11) |
| 19:41352821 | P>T | D:264 | (65.74, 101.40, 105.94) | |
| 19:41352817 | rs140471703 | R>Q | D:265 | (61.01, 99.26, 108.17) |
| 19:41352808 | I>T | D:268 | (61.43, 94.06, 102.43) | |
| 19:41352802 | rs560382680 COSM3797108 |
S>F | D:270 | (66.30, 97.99, 101.22) |
| 19:41352790 | rs139639589 | R>H | D:274 | (68.59, 98.98, 94.23) |
| 19:41352786 | rs111869995 | M>I | D:275 | (62.37, 98.38, 93.40) |
| 19:41352788 | M>L | D:275 | (62.37, 98.38, 93.40) | |
| 19:41351991 | N>K | D:281 | (66.59, 99.94, 84.18) | |
| 19:41351983 | rs201027514 COSM712827 |
T>M | D:284 | (65.89, 95.99, 86.48) |
| 19:41351978 | F>I | D:286 | (66.89, 95.21, 91.66) | |
| 19:41351974 | rs376990868 | Y>S | D:287 | (61.90, 92.38, 89.06) |
| 19:41351960 | rs2644906 | V>M | D:292 | (58.77, 87.95, 96.83) |
| 19:41351956 | M>T | D:293 | (60.60, 84.76, 95.21) | |
| 19:41351953 | rs4997557 | T>S | D:294 | (64.94, 86.87, 97.55) |
| 19:41351933 | COSM1393901 | G>R | D:301 | (67.20, 79.05, 104.54) |
| 19:41351924 | E>K | D:304 | (64.09, 74.16, 108.16) | |
| 19:41351918 | rs372113929 COSM566312 |
V>I | D:306 | (69.69, 76.05, 111.49) |
| 19:41351908 | rs528089983 | T>I | D:309 | (71.43, 71.23, 112.44) |
| 19:41351903 | rs58571639 | R>C | D:311 | (65.51, 68.57, 114.66) |
| 19:41351899 | Y>C | D:312 | (70.38, 64.70, 113.34) | |
| 19:41351885 | rs367912859 | L>F | D:317 | (74.38, 65.49, 122.37) |
| 19:41351878 | K>R | D:319 | (73.28, 57.88, 121.06) | |
| 19:41351861 | rs374963618 | A>P | D:325 | (80.01, 65.84, 129.61) |
| 19:41351383 | K>R | D:326 | (83.62, 65.97, 127.03) | |
| 19:41351377 | H>R | D:328 | (77.75, 70.21, 130.22) | |
| 19:41351375 | E>K | D:329 | (84.36, 70.76, 131.29) | |
| 19:41351370 | rs137904044 | E>D | D:330 | (84.44, 73.50, 127.28) |
| 19:41351361 | R>S | D:333 | (86.72, 75.30, 131.63) | |
| 19:41351359 | V>G | D:334 | (85.18, 79.01, 129.47) | |
| 19:41351344 | rs150247689 | R>Q | D:339 | (79.25, 84.73, 130.39) |
| 19:41351338 | P>L | D:341 | (76.94, 82.76, 125.77) | |
| 19:41351324 | rs141074424 | R>W | D:346 | (85.06, 80.93, 118.26) |
| 19:41351321 | rs200267449 | A>T | D:347 | (88.45, 80.46, 121.10) |
| 19:41351309 | rs148166815 | Y>H | D:351 | (84.59, 68.74, 122.69) |
| 19:41351304 | M>I | D:352 | (81.17, 73.18, 121.57) | |
| 19:41351305 | rs143841823 | M>T | D:352 | (81.17, 73.18, 121.57) |
| 19:41351306 | M>V | D:352 | (81.17, 73.18, 121.57) | |
| 19:41351300 | A>S | D:354 | (84.09, 69.90, 117.36) | |
| 19:41351288 | E>K | D:358 | (80.98, 65.63, 113.90) | |
| 19:41351270 | D>N | D:364 | (74.48, 65.48, 105.33) | |
| 19:41351267 | rs28399454 | V>M | D:365 | (71.23, 68.93, 106.19) |
| 19:41351263 | I>N | D:366 | (71.85, 69.87, 102.09) | |
| 19:41351256 | M>I | D:368 | (72.44, 65.92, 96.79) | |
| 19:41351257 | rs144689858 | M>T | D:368 | (72.44, 65.92, 96.79) |
| 19:41351250 | L>F | D:370 | (71.52, 73.49, 95.84) | |
| 19:41351251 | rs142447929 | L>S | D:370 | (71.52, 73.49, 95.84) |
| 19:41351245 | rs145036049 | R>H | D:372 | (76.55, 74.50, 91.02) |
| 19:41351246 | R>C | D:372 | (76.55, 74.50, 91.02) | |
| 19:41351227 | rs114558780 | T>I | D:378 | (83.35, 72.33, 80.37) |
| 19:41351218 | R>Q | D:381 | (88.69, 64.96, 86.29) | |
| 19:41351216 | rs372636737 | D>Y | D:382 | (89.64, 63.00, 80.81) |
| 19:41351209 | F>S | D:384 | (82.40, 68.06, 76.46) | |
| 19:41351207 | rs369136003 | L>F | D:385 | (80.66, 68.86, 80.72) |
| 19:41350673 | rs139066588 | T>I | D:389 | (75.36, 70.05, 82.11) |
| 19:41350668 | V>M | D:391 | (76.22, 69.43, 88.48) | |
| 19:41350664 | rs1809810 | F>Y | D:392 | (72.95, 66.36, 91.55) |
| 19:41350658 | M>T | D:394 | (77.23, 64.24, 96.24) | |
| 19:41350659 | M>V | D:394 | (77.23, 64.24, 96.24) | |
| 19:41350635 | P>S | D:402 | (87.45, 58.07, 103.52) | |
| 19:41350622 | S>C | D:406 | (88.65, 57.91, 110.70) | |
| 19:41350617 | P>S | D:408 | (83.14, 58.21, 108.32) | |
| 19:41350613 | rs59505316 | Q>R | D:409 | (79.70, 56.13, 108.71) |
| 19:41350611 | rs371553133 | D>Y | D:410 | (81.20, 56.82, 113.54) |
| 19:41350607 | F>Y | D:411 | (79.01, 61.94, 116.73) | |
| 19:41350608 | F>V | D:411 | (79.01, 61.94, 116.73) | |
| 19:41350602 | P>T | D:413 | (84.03, 64.81, 118.13) | |
| 19:41350587 | rs28399463 | N>D | D:418 | (94.68, 68.46, 117.63) |
| 19:41350581 | K>E | D:420 | (98.13, 69.08, 121.80) | |
| 19:41350575 | rs554920226 | Q>K | D:422 | (94.47, 72.27, 119.32) |
| 19:41350559 | D>G | D:427 | (89.88, 70.90, 103.13) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 19:41354554 | COSM189477 | A>V | D:153 | (68.51, 82.48, 123.25) |
| 19:41354538 | COSM1393905 | D>E | D:158 | (62.68, 81.70, 128.96) |
| 19:41354273 | COSM1304618 | D>N | D:169 | (58.69, 67.80, 119.74) |
| 19:41354251 | COSM379183 | R>H | D:176 | (58.92, 78.62, 117.84) |
| 19:41354171 | COSM328633 | R>S | D:203 | (53.38, 72.95, 111.31) |
| 19:41352955 | COSM1393902 | L>P | D:219 | (59.72, 60.23, 91.53) |
| 19:41351918 | COSM566312 | V>I | D:306 | (69.69, 76.05, 111.49) |
| 19:41351863 | COSM4140664 | E>G | D:324 | (76.07, 66.07, 127.51) |
| 19:41351219 | COSM996841 | R>W | D:381 | (88.69, 64.96, 86.29) |
| 19:41351203 | COSM1630938 | P>L | D:386 | (77.76, 69.99, 77.63) |
| 19:41350664 | COSM4591653 | F>Y | D:392 | (72.95, 66.36, 91.55) |
| 19:41349804 | COSM213661 | R>H | D:461 | (70.20, 67.78, 132.99) |
| 19:41349705 | COSM239507 | R>H | D:494 | (73.41, 72.27, 134.24) |