General Structure Information
| PDB ID | 4bc5 |
| HGNC Gene Label(s) | XYLB |
| Structure Name | crystal structure of human d-xylulokinase in complex with inhibitor 5-deoxy-5-fluoro-d-xylulose |
| Resolution | 1.98Å |
| Reference | AUTH R.D.BUNKER,E.M.M.BULLOCH,J.M.J.DICKSON,K.M.LOOMES,E.N.BAKERTITL STRUCTURE AND FUNCTION OF HUMAN XYLULOKINASE, AN ENZYMETITL 2 WITH IMPORTANT ROLES IN CARBOHYDRATE METABOLISMREF J.BIOL.CHEM. V. 288 1643 2013REFN ISSN 0021-9258PMID 23179721DOI 10.1074/JBC.M112.427997 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 526 |
| Number Of SNVs | 151 |
| Number Of Permutations | 27572 |
| Optimal Distance Threshold | 22.0 |
| K Statistic | 0.253 |
| p-value | 0.125 |
COSMIC
| Number Of Residues | 526 |
| Number Of SNVs | 7 |
| Number Of Permutations | 5181 |
| Optimal Distance Threshold | 5.0 |
| K Statistic | 0.048 |
| p-value | 0.803 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 151 |
| Number Of COSMIC SNVs | 6 |
| Optimal Distance Threshold | 34.0 |
| K Statistic | -0.257 |
| p-value | 0.366 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 3:38388375 | P>S | B:6 | (10.56, -36.24, -8.50) | |
| 3:38388378 | R>C | B:7 | (11.19, -35.26, -0.97) | |
| 3:38388381 | R>C | B:8 | (5.68, -36.52, -6.21) | |
| 3:38388390 | L>V | B:11 | (1.17, -35.92, 5.32) | |
| 3:38390048 | rs116150323 | V>G | B:22 | (2.82, -34.88, 10.97) |
| 3:38390050 | rs146884889 | V>I | B:23 | (5.24, -38.89, 9.93) |
| 3:38390054 | rs78669311 | A>V | B:24 | (6.42, -36.98, 5.76) |
| 3:38390056 | rs146134427 | V>L | B:25 | (6.24, -41.66, 4.44) |
| 3:38390081 | Y>C | B:33 | (8.74, -33.24, 8.21) | |
| 3:38390087 | E>G | B:35 | (6.61, -31.41, 13.31) | |
| 3:38390089 | S>G | B:36 | (5.12, -32.34, 17.13) | |
| 3:38390108 | D>A | B:42 | (2.43, -25.72, 22.58) | |
| 3:38401831 | rs200253546 COSM308438 |
T>A | B:48 | (-4.43, -29.57, 29.72) |
| 3:38401837 | G>R | B:50 | (-0.90, -34.57, 30.04) | |
| 3:38401838 | rs200329926 | G>D | B:50 | (-0.90, -34.57, 30.04) |
| 3:38401840 | rs149466325 | G>S | B:51 | (-3.29, -33.11, 27.75) |
| 3:38401858 | rs148604148 | D>H | B:57 | (-14.73, -37.34, 40.27) |
| 3:38401868 | rs146260536 | T>M | B:60 | (-14.68, -37.36, 34.65) |
| 3:38401874 | T>I | B:62 | (-12.35, -34.56, 29.83) | |
| 3:38401879 | rs115412959 | P>S | B:64 | (-10.13, -29.16, 25.74) |
| 3:38401883 | V>A | B:65 | (-13.20, -30.22, 20.87) | |
| 3:38401889 | M>T | B:67 | (-6.65, -28.72, 23.01) | |
| 3:38404452 | M>L | B:79 | (4.25, -28.70, 8.38) | |
| 3:38404470 | COSM278168 | D>N | B:85 | (6.74, -29.02, -0.40) |
| 3:38404472 | rs17118 | D>E | B:85 | (6.74, -29.02, -0.40) |
| 3:38404474 | rs375645376 | F>C | B:86 | (2.01, -28.59, 2.65) |
| 3:38404480 | Q>R | B:88 | (5.40, -32.55, -3.35) | |
| 3:38404495 | S>C | B:93 | (-4.36, -41.13, 6.66) | |
| 3:38404497 | G>R | B:94 | (-4.61, -41.02, 10.27) | |
| 3:38404504 | rs372561175 | G>D | B:96 | (-6.75, -41.62, 16.68) |
| 3:38404507 | Q>L | B:97 | (-6.77, -40.12, 21.26) | |
| 3:38406693 | rs139343226 | H>Y | B:99 | (-11.90, -45.89, 22.83) |
| 3:38406696 | G>R | B:100 | (-12.59, -40.73, 22.31) | |
| 3:38406700 | S>N | B:101 | (-16.12, -38.85, 21.92) | |
| 3:38406710 | W>C | B:104 | (-18.89, -32.07, 14.96) | |
| 3:38406729 | rs370702086 | A>S | B:111 | (-19.25, -24.30, 9.59) |
| 3:38406748 | rs375350114 | P>L | B:117 | (-8.86, -20.00, 2.55) |
| 3:38406760 | L>Q | B:121 | (-9.37, -25.19, 11.08) | |
| 3:38406762 | H>Y | B:122 | (-9.92, -22.10, 17.36) | |
| 3:38406775 | Q>R | B:126 | (-15.24, -20.21, 18.15) | |
| 3:38407109 | S>F | B:130 | (-22.73, -29.91, 21.68) | |
| 3:38407117 | rs2234610 | D>N | B:133 | (-15.04, -30.85, 27.99) |
| 3:38407145 | T>N | B:142 | (-18.90, -44.56, 32.24) | |
| 3:38407160 | rs148652538 | R>H | B:147 | (-23.71, -52.32, 33.63) |
| 3:38407165 | rs142877194 | L>M | B:149 | (-24.53, -51.46, 27.09) |
| 3:38407184 | COSM77038 | G>D | B:155 | (-24.82, -59.54, 29.20) |
| 3:38407190 | Q>R | B:157 | (-19.81, -63.40, 26.55) | |
| 3:38407192 | A>T | B:158 | (-23.88, -61.18, 25.03) | |
| 3:38407195 | L>F | B:159 | (-21.80, -56.11, 24.99) | |
| 3:38407198 | rs2234611 | S>R | B:160 | (-18.07, -59.53, 23.96) |
| 3:38407210 | G>R | B:164 | (-15.69, -57.83, 20.66) | |
| 3:38407216 | rs147965440 | R>C | B:166 | (-17.10, -57.31, 30.07) |
| 3:38407217 | rs200425508 | R>H | B:166 | (-17.10, -57.31, 30.07) |
| 3:38407223 | Y>C | B:168 | (-14.11, -52.84, 28.66) | |
| 3:38408299 | rs145351669 | R>C | B:170 | (-11.33, -47.72, 27.64) |
| 3:38408300 | rs200759971 COSM2155383 |
R>H | B:170 | (-11.33, -47.72, 27.64) |
| 3:38408303 | F>C | B:171 | (-14.77, -49.39, 24.81) | |
| 3:38408318 | rs377306222 | I>T | B:176 | (-22.59, -41.81, 23.33) |
| 3:38408330 | Y>C | B:180 | (-29.45, -39.67, 26.87) | |
| 3:38408333 | Q>R | B:181 | (-28.13, -41.06, 31.14) | |
| 3:38408336 | Q>R | B:182 | (-25.07, -36.93, 33.41) | |
| 3:38408344 | E>K | B:185 | (-30.36, -29.48, 26.51) | |
| 3:38408348 | A>V | B:186 | (-26.20, -31.19, 25.01) | |
| 3:38408354 | S>L | B:188 | (-30.92, -32.83, 22.00) | |
| 3:38408357 | H>R | B:189 | (-29.34, -29.10, 21.08) | |
| 3:38409692 | S>N | B:197 | (-10.21, -41.11, 14.40) | |
| 3:38409722 | rs199723335 | S>C | B:207 | (-17.12, -32.83, 5.24) |
| 3:38409728 | S>C | B:209 | (-15.45, -38.50, 8.25) | |
| 3:38409733 | rs367835960 | I>V | B:211 | (-17.08, -43.91, 12.70) |
| 3:38409738 | D>E | B:212 | (-13.20, -46.85, 10.50) | |
| 3:38411552 | G>R | B:218 | (-14.10, -49.28, 20.14) | |
| 3:38411556 | M>K | B:219 | (-17.91, -47.05, 19.78) | |
| 3:38411574 | Q>R | B:225 | (-19.94, -61.43, 12.10) | |
| 3:38411576 | D>N | B:226 | (-22.62, -58.29, 10.28) | |
| 3:38411577 | D>G | B:226 | (-22.62, -58.29, 10.28) | |
| 3:38411582 | rs141567257 | V>I | B:228 | (-24.17, -53.63, 10.66) |
| 3:38411589 | S>C | B:230 | (-25.73, -53.23, 17.50) | |
| 3:38411598 | C>Y | B:233 | (-25.85, -51.83, 21.31) | |
| 3:38411600 | L>F | B:234 | (-27.24, -47.97, 18.27) | |
| 3:38411615 | P>S | B:239 | (-32.06, -41.50, 22.31) | |
| 3:38411616 | rs139592452 | P>H | B:239 | (-32.06, -41.50, 22.31) |
| 3:38411640 | rs144298923 | P>L | B:247 | (-23.56, -45.34, 7.53) |
| 3:38411656 | rs140797435 | C>W | B:252 | (-8.83, -49.02, 2.93) |
| 3:38411658 | S>L | B:253 | (-12.17, -45.99, 2.68) | |
| 3:38414149 | A>T | B:257 | (-10.89, -34.76, -1.77) | |
| 3:38414153 | I>S | B:258 | (-7.27, -32.05, 1.05) | |
| 3:38414156 | S>Y | B:259 | (-10.83, -29.14, 2.15) | |
| 3:38414161 | rs147882141 | Y>H | B:261 | (-8.95, -24.32, 4.85) |
| 3:38414173 | rs374365370 COSM1044196 |
R>C | B:265 | (-4.54, -21.06, 5.49) |
| 3:38414174 | R>H | B:265 | (-4.54, -21.06, 5.49) | |
| 3:38414179 | rs546545439 | G>R | B:267 | (-0.88, -25.66, -1.04) |
| 3:38414182 | F>V | B:268 | (-2.29, -29.73, 1.27) | |
| 3:38415961 | rs146836764 | A>T | B:286 | (-0.69, -50.92, 9.85) |
| 3:38415964 | G>C | B:287 | (2.86, -49.84, 10.87) | |
| 3:38415965 | rs137889492 | G>V | B:287 | (2.86, -49.84, 10.87) |
| 3:38415992 | A>V | B:296 | (2.92, -57.48, 18.21) | |
| 3:38416671 | L>F | B:309 | (-7.70, -62.76, 15.71) | |
| 3:38416675 | rs200104408 | Q>R | B:310 | (-8.22, -65.26, 9.84) |
| 3:38416677 | E>K | B:311 | (-11.49, -67.64, 12.85) | |
| 3:38416685 | M>I | B:313 | (-13.15, -67.13, 19.37) | |
| 3:38416689 | rs372598292 | A>S | B:315 | (-13.65, -62.67, 25.68) |
| 3:38416704 | I>V | B:320 | (-11.91, -59.29, 19.11) | |
| 3:38416737 | M>V | B:331 | (-6.87, -56.07, 15.61) | |
| 3:38417622 | S>F | B:340 | (8.28, -52.61, 32.92) | |
| 3:38417633 | rs372268961 | E>Q | B:344 | (12.80, -52.65, 37.56) |
| 3:38417634 | E>A | B:344 | (12.80, -52.65, 37.56) | |
| 3:38417635 | E>D | B:344 | (12.80, -52.65, 37.56) | |
| 3:38417638 | rs535773969 | K>N | B:345 | (8.98, -54.42, 41.77) |
| 3:38417642 | R>C | B:347 | (16.91, -55.02, 37.79) | |
| 3:38417645 | rs2234622 | N>D | B:348 | (15.73, -54.26, 41.88) |
| 3:38417648 | rs140394832 | E>K | B:349 | (13.85, -58.22, 44.55) |
| 3:38417658 | rs367774221 | S>F | B:352 | (21.80, -57.17, 42.04) |
| 3:38417660 | rs556067053 | R>C | B:353 | (19.26, -53.06, 41.51) |
| 3:38417661 | R>H | B:353 | (19.26, -53.06, 41.51) | |
| 3:38417664 | S>C | B:354 | (22.22, -56.37, 37.15) | |
| 3:38417670 | S>N | B:356 | (24.01, -58.01, 33.00) | |
| 3:38417679 | S>F | B:359 | (20.64, -61.60, 30.86) | |
| 3:38417711 | G>S | B:370 | (12.59, -77.26, 36.12) | |
| 3:38418426 | M>L | B:380 | (-5.86, -56.18, 40.79) | |
| 3:38418438 | P>A | B:384 | (-6.00, -63.03, 34.50) | |
| 3:38418444 | I>V | B:386 | (-4.92, -63.20, 39.33) | |
| 3:38418448 | I>T | B:387 | (-3.78, -58.91, 43.47) | |
| 3:38418451 | COSM353214 | G>V | B:388 | (-0.28, -61.16, 43.81) |
| 3:38418453 | R>C | B:389 | (5.32, -61.31, 44.12) | |
| 3:38418454 | R>H | B:389 | (5.32, -61.31, 44.12) | |
| 3:38418456 | rs375435434 | H>Y | B:390 | (0.34, -66.26, 43.14) |
| 3:38418469 | T>I | B:394 | (8.16, -79.36, 40.10) | |
| 3:38418472 | E>G | B:395 | (5.20, -80.71, 42.41) | |
| 3:38420785 | Q>E | B:415 | (5.40, -61.92, 32.26) | |
| 3:38420798 | K>R | B:419 | (1.98, -61.89, 27.10) | |
| 3:38420801 | COSM1422733 | R>K | B:420 | (1.44, -69.84, 23.04) |
| 3:38420812 | E>K | B:424 | (-4.08, -69.52, 22.23) | |
| 3:38420821 | rs374612817 | G>S | B:427 | (-8.37, -67.60, 18.68) |
| 3:38420827 | rs573319439 | R>G | B:429 | (-5.00, -70.99, 17.56) |
| 3:38420828 | rs144082008 | R>Q | B:429 | (-5.00, -70.99, 17.56) |
| 3:38420830 | V>I | B:430 | (1.72, -70.20, 16.55) | |
| 3:38436999 | S>F | B:432 | (4.38, -72.32, 9.49) | |
| 3:38437019 | rs375509475 | T>S | B:439 | (8.20, -53.06, 20.53) |
| 3:38437025 | G>R | B:441 | (12.40, -51.70, 26.59) | |
| 3:38437046 | rs572431589 | I>V | B:448 | (13.73, -60.71, 28.08) |
| 3:38438569 | A>P | B:453 | (11.29, -67.18, 20.64) | |
| 3:38438572 | D>Y | B:454 | (11.60, -70.52, 23.30) | |
| 3:38438582 | D>G | B:457 | (7.88, -72.47, 18.62) | |
| 3:38438585 | A>D | B:458 | (8.06, -68.43, 16.61) | |
| 3:38438588 | P>L | B:459 | (10.52, -66.53, 14.12) | |
| 3:38438594 | rs148983928 | Y>C | B:461 | (11.69, -60.79, 13.19) |
| 3:38438597 | V>A | B:462 | (13.66, -56.05, 17.54) | |
| 3:38438613 | N>K | B:467 | (6.92, -42.46, 14.86) | |
| 3:38438615 | rs2234625 | S>L | B:468 | (3.94, -46.94, 15.21) |
| 3:38438617 | A>T | B:469 | (0.47, -44.52, 14.85) | |
| 3:38438626 | G>C | B:472 | (1.01, -46.64, 9.78) | |
| 3:38438630 | S>C | B:473 | (-1.25, -43.49, 9.27) | |
| 3:38438645 | F>S | B:478 | (1.95, -44.31, 0.14) | |
| 3:38442402 | rs2234627 | V>M | B:487 | (-4.02, -53.67, -4.09) |
| 3:38442405 | P>S | B:488 | (-2.68, -57.20, -1.42) | |
| 3:38442406 | P>L | B:488 | (-2.68, -57.20, -1.42) | |
| 3:38442417 | V>I | B:492 | (1.24, -51.41, -0.95) | |
| 3:38442463 | rs375440698 COSM3702417 |
P>L | B:507 | (17.06, -76.72, 19.64) |
| 3:38442469 | A>V | B:509 | (11.36, -75.21, 22.60) | |
| 3:38442472 | S>F | B:510 | (8.08, -77.52, 20.73) | |
| 3:38454427 | COSM583671 | V>I | B:512 | (9.96, -77.60, 27.17) |
| 3:38454433 | COSM1044202 | E>K | B:514 | (3.72, -78.29, 25.05) |
| 3:38454439 | L>F | B:516 | (5.59, -75.75, 31.30) | |
| 3:38454449 | Q>R | B:519 | (0.25, -76.51, 33.46) | |
| 3:38454485 | COSM3660517 | T>I | B:531 | (-9.28, -65.50, 44.34) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 3:38404472 | COSM4157998 | D>E | B:85 | (6.74, -29.02, -0.40) |
| 3:38404477 | COSM1309079 | S>F | B:87 | (2.93, -29.25, -3.62) |
| 3:38408326 | COSM1617540 | I>F | B:179 | (-22.70, -37.02, 27.14) |
| 3:38437009 | COSM1044198 | K>N | B:435 | (5.98, -63.71, 13.03) |
| 3:38438647 | COSM1692554 | H>Y | B:479 | (-3.32, -49.85, 0.54) |
| 3:38442432 | COSM1722963 | P>S | B:497 | (11.81, -49.88, 6.52) |
| 3:38454485 | COSM3660517 | T>I | B:531 | (-9.28, -65.50, 44.34) |