Receptor
PDB id Resolution Class Description Source Keywords
5IXJ 1.54 Å EC: 4.2.1.20 TRYPTOPHAN SYNTHASE BETA-SUBUNIT FROM PYROCOCCUS FURIOSUS WI THREONINE NON-COVALENTLY BOUND IN THE ACTIVE SITE PYROCOCCUS FURIOSUS (STRAIN ATCC 435873638 / JCM 8422 / VC1) SUBSTRATE ANALOG LYASE PLP FOLD-TYPE II
Ref.: SYNTHESIS OF BETA-BRANCHED TRYPTOPHAN ANALOGUES USI ENGINEERED SUBUNIT OF TRYPTOPHAN SYNTHASE. J.AM.CHEM.SOC. V. 138 8388 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NA B:402;
C:402;
D:402;
A:402;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
22.99 Na [Na+]
THR D:401;
A:401;
B:401;
C:401;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
119.119 C4 H9 N O3 C[C@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5IXJ 1.54 Å EC: 4.2.1.20 TRYPTOPHAN SYNTHASE BETA-SUBUNIT FROM PYROCOCCUS FURIOSUS WI THREONINE NON-COVALENTLY BOUND IN THE ACTIVE SITE PYROCOCCUS FURIOSUS (STRAIN ATCC 435873638 / JCM 8422 / VC1) SUBSTRATE ANALOG LYASE PLP FOLD-TYPE II
Ref.: SYNTHESIS OF BETA-BRANCHED TRYPTOPHAN ANALOGUES USI ENGINEERED SUBUNIT OF TRYPTOPHAN SYNTHASE. J.AM.CHEM.SOC. V. 138 8388 2016
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5DW3 - TRP C11 H12 N2 O2 c1ccc2c(c1....
2 5T6M - 78U C12 H14 N2 O2 C[C@@H](c1....
3 5DW0 - PLS C11 H17 N2 O8 P Cc1c(c(c(c....
4 5IXJ - THR C4 H9 N O3 C[C@H]([C@....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5DW3 - TRP C11 H12 N2 O2 c1ccc2c(c1....
2 5T6M - 78U C12 H14 N2 O2 C[C@@H](c1....
3 5DW0 - PLS C11 H17 N2 O8 P Cc1c(c(c(c....
4 5IXJ - THR C4 H9 N O3 C[C@H]([C@....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5DW3 - TRP C11 H12 N2 O2 c1ccc2c(c1....
2 5T6M - 78U C12 H14 N2 O2 C[C@@H](c1....
3 5DW0 - PLS C11 H17 N2 O8 P Cc1c(c(c(c....
4 5IXJ - THR C4 H9 N O3 C[C@H]([C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: THR; Similar ligands found: 11
No: Ligand ECFP6 Tc MDL keys Tc
1 THR 1 1
2 VAL 0.65 0.714286
3 DAL 0.578947 0.789474
4 ALA 0.578947 0.789474
5 VAH 0.541667 0.76
6 ILE 0.541667 0.6
7 HGY 0.526316 0.625
8 AHB 0.5 0.6
9 ABA 0.434783 0.625
10 DBB 0.434783 0.625
11 LFC 0.407407 0.619048
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5IXJ; Ligand: THR; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5ixj.bio2) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5IXJ; Ligand: THR; Similar sites found: 145
This union binding pocket(no: 2) in the query (biounit: 5ixj.bio2) has 32 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5XCZ GLC BGC 0.03376 0.40393 1.39665
2 3V0H I3P 0.01843 0.422 1.47493
3 3NZ1 3NY 0.02928 0.41262 1.51515
4 3I27 SID 0.008859 0.43897 1.5625
5 2NSX IFM 0.008304 0.42703 1.76768
6 4M00 SUC 0.03706 0.40494 1.76768
7 3KC1 2T6 0.01358 0.40271 1.78042
8 3PIJ FRU 0.02957 0.41099 2.0202
9 4X1B MLI 0.04907 0.40321 2.0202
10 5H9I XAN 0.01927 0.41929 2.08333
11 4EVQ PHB 0.02154 0.41021 2.13333
12 3JU6 ARG 0.03339 0.40557 2.16216
13 5DT6 GLU 0.03244 0.41093 2.24719
14 1EYQ NAR 0.02746 0.40864 2.25225
15 2DHC DCE 0.02791 0.41127 2.25806
16 4IP7 FBP 0.003325 0.4381 2.27273
17 3N6M GTP 0.02296 0.41271 2.27273
18 2WZF BGC 0.0348 0.40767 2.27273
19 2QGI UDP 0.03805 0.40602 2.41935
20 2JK0 ASP 0.01566 0.4266 2.46154
21 4RF7 ARG 0.002056 0.4665 2.52525
22 4WXJ GLU 0.02713 0.413 2.60223
23 1IK4 PGH 0.02661 0.40193 2.63158
24 4NAE 1GP 0.0338 0.40812 2.66667
25 5A2Z GTP 0.02427 0.41145 2.77778
26 1B57 PGH 0.01667 0.41587 2.7933
27 1SW0 PGA 0.003713 0.44429 2.82258
28 1CZR FMN 0.01498 0.40076 2.95858
29 3AJ6 NGA 0.024 0.41124 3.0303
30 2CHN NGT 0.0227 0.4019 3.0303
31 3WVR AMP 0.02385 0.40085 3.0303
32 1W8S FBP 0.01393 0.41221 3.04183
33 1J1R ADE 0.04616 0.40121 3.06513
34 4YSX MLI 0.03924 0.4048 3.20513
35 3OPT AKG 0.04478 0.402 3.21716
36 4NTX AMR 0.002683 0.46953 3.28283
37 1T9D PYD 0.01729 0.41125 3.28283
38 4BHL ARG 0.004372 0.44747 3.37079
39 4BG4 ARG 0.0113 0.43438 3.37079
40 2R09 4IP 0.02694 0.41316 3.45821
41 2XBL M7P 0.01303 0.41007 3.53535
42 5EYW PGA 0.002417 0.46345 3.61446
43 5EI3 5O8 0.04107 0.40257 3.68664
44 1M5W DXP 0.01395 0.42846 3.7037
45 2FAH MLA 0.03523 0.40689 3.78788
46 2POC UD1 0.03335 0.40421 3.81471
47 4N82 FMN 0.0119 0.40854 3.93258
48 2AWN ADP 0.03761 0.40896 3.93701
49 2D2F ADP 0.01392 0.44043 4
50 1X8X TYR 0.03048 0.40251 4.03727
51 2BES RES 0.009559 0.42401 4.06977
52 1GT6 OLA 0.01618 0.40905 4.08922
53 2DVZ GLU 0.006776 0.4357 4.14013
54 4WOH 4NP 0.01639 0.41734 4.21687
55 5EXK MET 0.04788 0.40027 4.22961
56 5O4F 8VE 0.03405 0.40374 4.26357
57 3TTN SPD 0.01644 0.42552 4.41176
58 3AVS OGA 0.03368 0.40399 4.54545
59 3VPC ADP 0.005313 0.41455 4.60993
60 2ZX2 RAM 0.02893 0.40814 4.61538
61 2HIM ASN 0.02855 0.41262 4.7486
62 3HQP FDP 0.02594 0.40609 4.79798
63 2JIG PD2 0.01665 0.41999 4.91071
64 2WPB ZZI 0.01889 0.42143 4.93421
65 4BWL MN9 0.0224 0.41844 4.93421
66 1S8G DAO 0.02301 0.40508 4.95868
67 1VB3 KPA 0.003256 0.46207 5.05051
68 1SW1 PBE 0.03681 0.40238 5.09091
69 2F5X ASP 0.01003 0.43611 5.12821
70 4NS0 PIO 0.005436 0.43618 5.26316
71 4JWX 1N4 0.01631 0.42484 5.35714
72 4WOE 3S5 0.02899 0.40058 5.55556
73 2PZE ATP 0.01968 0.42642 5.67686
74 1UWC FER 0.0339 0.40383 5.74713
75 3RGQ 5P5 0.04038 0.4048 5.76923
76 5DNC ASN 0.003924 0.45256 5.80808
77 4R8L ASP 0.005287 0.44586 5.97403
78 5CGE 51F 0.03459 0.40338 6.13718
79 3K7S R52 0.004451 0.44492 6.14525
80 1X0P FAD 0.02151 0.40304 6.29371
81 3V2U GLA 0.02825 0.40063 6.31313
82 5NTD BES 0.02424 0.40051 6.31313
83 3BF1 PAU 0.02062 0.40744 6.4257
84 4D9C PMP 0.000405 0.45151 6.43275
85 4K7O EKZ 0.03381 0.40619 6.54762
86 4Y8D 49J 0.03011 0.41056 6.76471
87 2PEL LAT 0.02134 0.41982 6.77966
88 2OS2 OGA 0.04034 0.40453 6.82415
89 1JJ7 ADP 0.04436 0.40813 6.92308
90 4XFR CIT 0.03894 0.40806 7.02576
91 4YC9 4C1 0.01924 0.40894 7.06522
92 1U1J MET 0.02133 0.42499 7.32323
93 2Q8E OGA 0.0397 0.405 7.38636
94 1G6H ADP 0.03507 0.40751 7.393
95 4KAX 4IP 0.0349 0.40711 7.45342
96 1I7Q PYR 0.03833 0.41148 7.77202
97 4UP4 NDG 0.0283 0.419 7.82828
98 2IW3 ADP 0.03176 0.40159 7.82828
99 5IFK HPA 0.04292 0.40105 8.01282
100 1OHE ACE ALA SEP PRO 0.042 0.40276 8.04598
101 4B2D FBP 0.001819 0.45045 8.33333
102 2OHH FMN 0.008257 0.40044 8.33333
103 3D78 NBB 0.006924 0.40654 8.40336
104 2I6U NVA 0.042 0.40276 8.46906
105 5GVR LMR 0.01553 0.44088 8.54701
106 5TG5 JW8 0.0412 0.40335 8.57143
107 2A9G ARG 0.03136 0.40562 8.58586
108 3QH2 3NM 0.03493 0.40709 8.59729
109 5NUL FMN 0.00234 0.4412 8.69565
110 2AKO ADP 0.01299 0.41013 8.76494
111 1X9I G6Q 0.01641 0.41238 8.9404
112 1WAP TRP 0.01756 0.40733 9.33333
113 1FUT 2GP 0.01317 0.43193 9.43396
114 3PH4 AOS 0.02946 0.40704 9.46746
115 4D9M 0JO 0.000005122 0.53989 9.59596
116 2J5V RGP 0.006578 0.44263 10.0817
117 1V7C HEY 0.00008107 0.46837 10.5413
118 2VHL GLP 0.01772 0.41453 10.6061
119 3ZO7 K6H 0.03784 0.40132 10.6383
120 3O5N BR0 0.02761 0.42355 10.7143
121 3HEE R5P 0.02738 0.4087 10.7383
122 3HP8 SUC 0.03715 0.40717 10.9091
123 3I9U DTU 0.01133 0.43403 11.0266
124 5CSS G3P 0.03767 0.40143 11.0619
125 4U00 ADP 0.03658 0.41343 11.0656
126 3PC3 P1T 0.0001765 0.47877 12.1212
127 3W6X HZP 0.04692 0.40047 12.6638
128 1FQK ALF 0.03854 0.40531 12.9252
129 5X2N ALA 0.0302 0.40849 13.3838
130 4H2D FMN 0.0135 0.40934 14.5455
131 2FCR FMN 0.006394 0.4247 15.0289
132 3GNE FLC 0.03582 0.4065 15.0794
133 3LN9 FLC 0.002064 0.48107 15.1079
134 3CV2 OXL 0.01713 0.42289 15.1515
135 5B3A 0JO 0.0001177 0.48194 16.4524
136 1VBO MAN 0.005972 0.4533 18.7919
137 1VBO MAN MAN MAN 0.01728 0.42501 18.7919
138 5D6J ATP 0.008585 0.41175 21.6216
139 1J0D 5PA 0.0006003 0.43773 23.7537
140 2PS1 ORO 0.02197 0.41371 23.8938
141 3L6C MLI 0.000156 0.52906 24.4838
142 4JBL MET 0.002925 0.46455 35.1032
143 1D6S PLP MET 0.00004664 0.49905 38.8199
144 1D6S MET PLP 0.0000585 0.49034 38.8199
145 3VC3 C6P 0.00006118 0.48102 39.5349
Pocket No.: 3; Query (leader) PDB : 5IXJ; Ligand: THR; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5ixj.bio1) has 32 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5IXJ; Ligand: THR; Similar sites found: 48
This union binding pocket(no: 4) in the query (biounit: 5ixj.bio1) has 40 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2WQN ADP 0.03413 0.40481 1.29032
2 2PCU ASP 0.03781 0.40957 1.96721
3 3TTM PUT 0.007839 0.44336 2.31214
4 1GZF NIR 0.04022 0.41197 2.36967
5 2VPN 4CS 0.02201 0.42811 2.53165
6 5KY4 GDP 0.02089 0.41946 2.53521
7 5KY9 GDP 0.0366 0.40001 2.53521
8 5KXQ GDP 0.04011 0.4012 2.54237
9 4MNP SLB 0.02645 0.41049 2.5641
10 3BF8 MLA 0.04233 0.40941 2.7451
11 4WNP 3RJ 0.04118 0.40061 2.78746
12 3BRE C2E 0.02108 0.42547 2.7933
13 2IYL GDP 0.02799 0.4128 2.8169
14 1A99 PUT 0.009544 0.44371 2.90698
15 1P7T PYR 0.02534 0.41323 3.28283
16 4ZLA BES 0.02561 0.4078 3.28283
17 4XJ7 ADN 0.04158 0.40039 3.37079
18 3AKI AH8 0.03428 0.40144 3.53535
19 1KSK URA 0.046 0.40312 3.84615
20 1SM4 FAD 0.02562 0.40456 4.05405
21 1YRX FMN 0.02069 0.40912 4.13223
22 3QX9 ATP 0.04109 0.4122 4.34783
23 4UY1 TJM 0.04226 0.40338 4.58015
24 2MAS PIR 0.03093 0.40055 4.77707
25 1WK9 TSB 0.0397 0.40143 4.79452
26 2X7I CIT 0.02646 0.41408 4.87013
27 3OCP CMP 0.02228 0.418 5.03597
28 2PHX MAN MAN 0.03123 0.41779 5.30303
29 2GNM MAN 0.02474 0.41578 5.30303
30 4XZ3 ACP 0.04179 0.41105 5.30303
31 1UKG MMA 0.03895 0.40706 5.30303
32 4NV0 MG7 0.02944 0.40811 5.64263
33 1WUU GLA 0.04857 0.40831 5.76441
34 5T96 79J 0.04366 0.40037 5.84795
35 3MMH SME 0.03929 0.40505 5.98802
36 1RDS GPC 0.02481 0.40849 6.66667
37 2BTM PGA 0.006055 0.45209 7.93651
38 4BHN BH9 0.01725 0.40373 9.88024
39 3N9R TD3 0.04143 0.40384 10.4235
40 1N4K I3P 0.04601 0.40662 11.0236
41 2W5P CL8 0.02606 0.42257 11.4094
42 5KY5 GDP 0.03251 0.40589 12.5
43 4HBM 0Y7 0.02889 0.402 13.3333
44 4C2W ANP 0.04506 0.40191 15.3846
45 5FUI APY 0.02592 0.40606 18.1818
46 2IMG MLT 0.01498 0.43479 19.8675
47 5JH2 A2P 0.04313 0.40648 23.871
48 5W97 CHD 0.03966 0.41309 32.1101
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