Receptor
PDB id Resolution Class Description Source Keywords
4ZU4 1.7 Å EC: 5.-.-.- X-RAY STRUCTURE OF THE 3,4-KETOISOMERASE DOMAIN OF FDTD FROM SHEWANELLA DENITRIFICANS SHEWANELLA DENITRIFICANS (STRAIN OS217BAA-1090 / DSM 15013) CUPIN KETOISOMERASE LIPOPOLYSACCHARIDE ISOMERASE
Ref.: BACTERIAL SUGAR 3,4-KETOISOMERASES: STRUCTURAL INSI PRODUCT STEREOCHEMISTRY. BIOCHEMISTRY V. 54 4495 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
4TG B:401;
C:401;
A:401;
Valid;
Valid;
Valid;
none;
none;
Atoms found MORE than expected: % Diff = 2;
submit data
575.355 C17 H27 N3 O15 P2 C[C@@...
CL D:401;
A:402;
F:401;
B:402;
D:402;
E:401;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
35.453 Cl [Cl-]
EDO E:402;
A:403;
A:404;
F:402;
E:403;
B:403;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
NA C:402;
A:405;
Part of Protein;
Part of Protein;
none;
none;
submit data
22.99 Na [Na+]
PO4 E:404;
Invalid;
none;
submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4ZU4 1.7 Å EC: 5.-.-.- X-RAY STRUCTURE OF THE 3,4-KETOISOMERASE DOMAIN OF FDTD FROM SHEWANELLA DENITRIFICANS SHEWANELLA DENITRIFICANS (STRAIN OS217BAA-1090 / DSM 15013) CUPIN KETOISOMERASE LIPOPOLYSACCHARIDE ISOMERASE
Ref.: BACTERIAL SUGAR 3,4-KETOISOMERASES: STRUCTURAL INSI PRODUCT STEREOCHEMISTRY. BIOCHEMISTRY V. 54 4495 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 26 families.
1 4ZU4 - 4TG C17 H27 N3 O15 P2 C[C@@H]1[C....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 24 families.
1 4ZU4 - 4TG C17 H27 N3 O15 P2 C[C@@H]1[C....
50% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 4ZU4 - 4TG C17 H27 N3 O15 P2 C[C@@H]1[C....
2 2PA7 - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
3 2PAM - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
4 2PAK - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
5 2PAE - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
6 5TPU - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
7 4O9G - T46 C16 H24 N2 O15 P2 C[C@@H]1C(....
8 4ZU7 - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
9 4O9E - TDR C5 H6 N2 O2 CC1=CNC(=O....
10 4ZU5 - THM C10 H14 N2 O5 CC1=CN(C(=....
11 5TPV - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 4TG; Similar ligands found: 57
No: Ligand ECFP6 Tc MDL keys Tc
1 4TG 1 1
2 1YF 0.785714 1
3 FNF 0.785714 1
4 TRH 0.768421 0.986486
5 18T 0.768421 0.986486
6 1JB 0.768421 0.986486
7 0FX 0.737374 0.986667
8 MMF 0.72 0.986667
9 T3F 0.717172 0.986667
10 T3Q 0.717172 0.986667
11 DAU 0.69 0.96
12 QDM 0.68932 0.948052
13 TDX 0.68 0.972973
14 T46 0.676471 0.986486
15 FUH 0.663636 0.986667
16 QUH 0.663636 0.986667
17 TTP 0.631579 0.92
18 3R2 0.631068 0.947368
19 0N2 0.628571 0.973684
20 TYD 0.623656 0.92
21 3YN 0.619048 0.96
22 DWN 0.603774 0.960526
23 T5K 0.578125 0.902439
24 T4K 0.578125 0.902439
25 TLO 0.576923 0.921053
26 JHZ 0.576577 0.935897
27 AKM 0.576577 0.936709
28 TQP 0.570312 0.890244
29 7SG 0.570312 0.890244
30 TMP 0.569892 0.906667
31 T5A 0.496 0.86747
32 TBD 0.485437 0.884615
33 0DN 0.473118 0.789474
34 AZD 0.458716 0.8625
35 DT DT PST 0.457627 0.884615
36 DT DT DT DT DT 0.456897 0.921053
37 THM 0.451613 0.826667
38 LLT 0.451613 0.826667
39 UFP 0.45 0.835443
40 ATY 0.440367 0.921053
41 5HU 0.431373 0.894737
42 ATM 0.429907 0.85
43 THP 0.423077 0.893333
44 TPE 0.420168 0.922078
45 T3P 0.42 0.868421
46 4TA 0.41791 0.833333
47 BRU 0.417476 0.835443
48 DUT 0.416667 0.88
49 D3T 0.416667 0.894737
50 5IU 0.413462 0.835443
51 FDM 0.413462 0.848101
52 NYM 0.413462 0.907895
53 TXS 0.407767 0.772152
54 DUD 0.40566 0.88
55 DT ME6 DT 0.40458 0.873418
56 BVP 0.40367 0.87013
57 T3S 0.4 0.794872
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4ZU4; Ligand: 4TG; Similar sites found: 130
This union binding pocket(no: 1) in the query (biounit: 4zu4.bio2) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5EW9 5VC 0.004394 0.47637 None
2 4WN5 MVC 0.00364 0.42557 None
3 3MWS 017 0.01495 0.40845 None
4 2BOS GLA GAL GLC 0.0114 0.40653 None
5 3GZ8 APR 0.009228 0.4054 None
6 2BOS GLA GAL 0.01277 0.40292 None
7 1SN0 T44 0.01111 0.40172 None
8 1M6P M6P 0.005937 0.42839 1.35135
9 5IXH OTP 0.01805 0.41481 1.35135
10 4MJ0 SIA SIA GAL 0.02048 0.40383 1.35135
11 4MJ0 BGC SIA SIA GAL 0.02109 0.40323 1.35135
12 5D3X 4IP 0.007691 0.42186 2.02703
13 5AAV GW5 0.04868 0.40161 2.02703
14 4AZP A9M 0.01347 0.40111 2.17391
15 3ZXE PGZ 0.0004396 0.40248 2.25564
16 5FPX GLY SER SER HIS HIS HIS HIS HIS 0.00001005 0.50849 2.65487
17 3H7J PPY 0.000522 0.45819 2.7027
18 4BVA T3 0.003788 0.44499 2.7027
19 1DZK PRZ 0.00148 0.43766 2.7027
20 4AZT LY2 0.002631 0.43562 2.7027
21 4QM9 CYS 0.006594 0.4241 2.7027
22 4Y24 TD2 0.0009808 0.4232 2.7027
23 3SAO NKN 0.00116 0.42051 2.7027
24 5N87 N66 0.01084 0.41858 2.7027
25 1Y0G 8PP 0.02653 0.40655 2.7027
26 3OYW TDG 0.003047 0.44295 2.98507
27 2HKA C3S 0.003676 0.40523 3.07692
28 1KGI T4A 0.002195 0.43736 3.14961
29 4K55 H6P 0.0001286 0.51772 3.22581
30 3H9A PPY 0.001475 0.40482 3.29218
31 1GP6 QUE 0.001333 0.4507 3.37838
32 1GP6 SIN 0.001298 0.44957 3.37838
33 1GP6 DH2 0.001298 0.44957 3.37838
34 2YG2 FLC 0.002691 0.43656 3.37838
35 2YG2 S1P 0.002358 0.43418 3.37838
36 1IF7 SBR 0.02698 0.43074 3.37838
37 5U98 1KX 0.01038 0.42471 3.37838
38 1DMY AZM 0.007468 0.41853 3.37838
39 1EPB REA 0.003487 0.41664 3.37838
40 2Z5Y HRM 0.01305 0.40663 3.37838
41 4WVW SLT 0.0001478 0.51952 3.47222
42 1Y2F WAI 0.02046 0.40165 3.59712
43 4XCB HY0 0.001393 0.44982 4.05405
44 4NFN 2KC 0.001159 0.43785 4.05405
45 4GJY OGA 0.00511 0.4316 4.05405
46 4USF 6UI 0.007326 0.4133 4.05405
47 5DEY 59T 0.02847 0.4114 4.05405
48 2VFT SOR 0.009951 0.40805 4.05405
49 3FW3 ETS 0.01195 0.40424 4.05405
50 5H9P TD2 0.001607 0.40331 4.05405
51 5DG2 GAL GLC 0.005091 0.40255 4.44444
52 2YMZ LAT 0.007029 0.41369 4.61538
53 4TW7 37K 0.008241 0.41401 4.6875
54 5ML3 DL3 0.001254 0.46593 4.72973
55 4X5S AZM 0.00331 0.44613 4.72973
56 3L9R L9Q 0.008088 0.42354 4.72973
57 3L9R L9R 0.01098 0.42049 4.72973
58 2WT2 GAL NAG GAL NAG GAL NAG 0.008176 0.41267 4.72973
59 5JKG 6LF 0.02306 0.40486 4.72973
60 2XMY CDK 0.003343 0.46569 5.40541
61 1GT4 UNA 0.001968 0.42766 5.40541
62 5W4W 9WG 0.006508 0.41567 5.40541
63 4Q0L V14 0.01269 0.40382 5.40541
64 1DZT TPE 0.000394 0.49395 6.08108
65 4B7P 9UN 0.0126 0.42515 6.08108
66 3Q8G PEE 0.01847 0.42236 6.08108
67 1ZM1 BGC BGC BGC 0.005254 0.40874 6.08108
68 5EPQ OLA 0.006379 0.405 6.08108
69 4EIP FAD 0.03705 0.40338 6.08108
70 4EIP K2C 0.03705 0.40338 6.08108
71 2R5V HHH 0.01122 0.40152 6.08108
72 4MNS 2AX 0.000356 0.50362 6.75676
73 4OPC PGT 0.002949 0.48833 6.75676
74 4OPC FDA 0.003778 0.4794 6.75676
75 2D6M LBT 0.001434 0.45539 6.75676
76 2AG4 OLA 0.01303 0.43146 6.75676
77 2AG4 LP3 0.01432 0.43146 6.75676
78 5A3T MMK 0.004836 0.43042 6.75676
79 3E8T UQ8 0.01968 0.42168 6.75676
80 5UR1 YY9 0.01824 0.41367 6.75676
81 5T7I LAT NAG GAL 0.007984 0.42383 7.43243
82 5IXG OTP 0.02837 0.40762 7.43243
83 3X1Z GNP 0.01567 0.40101 7.43243
84 1OGA GLY ILE LEU GLY PHE VAL PHE THR LEU 0.04144 0.40016 7.43243
85 1A78 TDG 0.007853 0.41773 7.46269
86 5FU3 BGC BGC BGC 0.006203 0.42966 7.54717
87 4QPW XYP XYP XYP 0.0005448 0.4311 7.74648
88 3MTX PGT 0.0007622 0.4697 8.10811
89 5BYZ 4WE 0.003725 0.43577 8.10811
90 1LSH PLD 0.006201 0.424 8.10811
91 3QUZ QUV 0.02605 0.41335 8.10811
92 3G08 FEE 0.02819 0.41305 8.10811
93 4OMJ 2TX 0.01345 0.41182 8.10811
94 4QJP V1F 0.01025 0.40813 8.10811
95 3SCM LGN 0.0371 0.40767 8.10811
96 3MKH FAD 0.02136 0.40545 8.10811
97 4P5Z Q7M 0.02496 0.40318 8.10811
98 2IXC TRH 0.0000342 0.5158 8.78378
99 2A1L PCW 0.001607 0.46732 8.78378
100 5UQD AKG 0.003199 0.4432 8.78378
101 5CJF 520 0.007356 0.41006 8.78378
102 5EOB 5QQ 0.03541 0.40732 8.78378
103 5TFZ 7BC 0.0002891 0.48759 9.45946
104 4DSU BZI 0.00216 0.45703 9.52381
105 5KEW 6SB 0.0002382 0.50346 9.57447
106 1MHC FME TYR PHE ILE ASN ILE LEU THR LEU 0.001672 0.45747 10.1351
107 3AGC RCC 0.002971 0.43611 10.1351
108 3T1A 5MA 0.008076 0.40443 10.1351
109 4Y3O OGA 0.02391 0.40022 10.1351
110 2GJ5 VD3 0.001919 0.45703 10.8108
111 5DQ8 FLF 0.003518 0.42795 10.8108
112 1P0Z FLC 0.02046 0.40312 11.4504
113 4YRD 3IT 0.0000008794 0.63109 11.4865
114 4RFR RHN 0.0005136 0.45817 11.4865
115 5F3I 5UJ 0.01756 0.42346 11.4865
116 1LRH NLA 0.002198 0.40995 12.1622
117 3MHA Z69 0.01251 0.40697 12.1622
118 2GC0 PAN 0.0001738 0.46571 12.8378
119 2XCG XCG 0.01128 0.41303 13.5135
120 1GQG DCD 0.001162 0.44821 14.1892
121 1TT8 PHB 0.0007521 0.46222 14.8649
122 4YLZ LAT NAG GAL 0.0009352 0.40507 14.8649
123 5JSP DQY 0.0005717 0.41195 15.5405
124 1N5S ADL 0.005761 0.40697 19.6429
125 1J3R 6PG 0.0006898 0.43115 20.2703
126 1KJ1 MAN 0.007749 0.42846 22.0183
127 3AVR OGA 0.01701 0.40659 22.7273
128 5FLJ QUE 0.002 0.4356 22.973
129 1NYW DAU 0.0000007204 0.58613 24.3243
130 5L2J 70E 0.04442 0.40978 28.3784
Pocket No.: 2; Query (leader) PDB : 4ZU4; Ligand: 4TG; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4zu4.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4ZU4; Ligand: 4TG; Similar sites found: 36
This union binding pocket(no: 3) in the query (biounit: 4zu4.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4PSB GA3 0.003833 0.43145 None
2 2XXP DSL 0.01808 0.42497 2.02703
3 1W6O LAT 0.01201 0.41566 2.98507
4 3FW4 CAQ 0.01002 0.40181 3.37838
5 3HAV ATP 0.01064 0.422 4.05405
6 2ZHL NAG GAL GAL NAG 0.006187 0.41761 4.05405
7 4RYV ZEA 0.0007525 0.41249 4.05405
8 2CM4 RCL 0.005806 0.40734 4.05405
9 4FHD 0TT 0.01357 0.40394 4.05405
10 4FHD EEM 0.01357 0.40394 4.05405
11 5C5T AKG 0.0198 0.40147 4.05405
12 3KFF XBT 0.01092 0.41896 4.72973
13 3KFF ZBT 0.01092 0.41896 4.72973
14 5IH9 6BF 0.01203 0.40979 4.72973
15 5FWJ MMK 0.01885 0.40253 4.72973
16 4BVM VCA 0.008415 0.402 5.26316
17 4BVM PLM 0.007698 0.402 5.26316
18 3KRR DQX 0.008665 0.43703 5.40541
19 4DE9 VTP 0.01372 0.40251 5.40541
20 5BVE 4VG 0.02067 0.41716 6.08108
21 5VC5 96M 0.006758 0.41237 6.08108
22 4TWP AXI 0.02965 0.41191 6.08108
23 1ZB6 GST 0.009643 0.40817 6.08108
24 2FB3 GTP 0.01102 0.40556 6.08108
25 3E85 BSU 0.0003395 0.48613 7.43243
26 1A99 PUT 0.02347 0.40692 8.10811
27 1QD1 FON 0.008863 0.40417 8.10811
28 3B00 16A 0.01193 0.40817 10.1351
29 5FQ0 FLC 0.01579 0.41041 10.5263
30 5C3R AKG 0.00717 0.40314 10.8108
31 5C3R HMU 0.00717 0.40314 10.8108
32 1QKQ MAN 0.001632 0.47545 11.2676
33 3HQR OGA 0.008388 0.41137 12.1622
34 3PUR 2HG 0.02573 0.40099 12.8378
35 1FDQ HXA 0.005888 0.41647 12.9771
36 3E2M E2M 0.0009572 0.40598 22.973
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