Receptor
PDB id Resolution Class Description Source Keywords
5B4B 1.6 Å EC: 3.6.1.54 CRYSTAL STRUCTURE OF LPXH WITH LIPID X IN SPACEGROUP C2 PSEUDOMONAS AERUGINOSA PAO1 LPXH LIPID A LIPID X UDP-2 3-DIACYLGLUCOSAMINE HYDROLAS
Ref.: CRYSTAL STRUCTURES OF THE UDP-DIACYLGLUCOSAMINE PYROPHOSPHOHYDRASE LPXH FROM PSEUDOMONAS AERUGINOSA SCI REP V. 6 32822 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
LP5 B:301;
A:301;
Valid;
Valid;
none;
Atoms found MORE than expected: % Diff = 2;
submit data
711.861 C34 H66 N O12 P CCCCC...
GOL A:302;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5B4B 1.6 Å EC: 3.6.1.54 CRYSTAL STRUCTURE OF LPXH WITH LIPID X IN SPACEGROUP C2 PSEUDOMONAS AERUGINOSA PAO1 LPXH LIPID A LIPID X UDP-2 3-DIACYLGLUCOSAMINE HYDROLAS
Ref.: CRYSTAL STRUCTURES OF THE UDP-DIACYLGLUCOSAMINE PYROPHOSPHOHYDRASE LPXH FROM PSEUDOMONAS AERUGINOSA SCI REP V. 6 32822 2016
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5B4A - LP5 C34 H66 N O12 P CCCCCCCCCC....
2 5B49 - LP5 C34 H66 N O12 P CCCCCCCCCC....
3 5B4B - LP5 C34 H66 N O12 P CCCCCCCCCC....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5B4A - LP5 C34 H66 N O12 P CCCCCCCCCC....
2 5B49 - LP5 C34 H66 N O12 P CCCCCCCCCC....
3 5B4B - LP5 C34 H66 N O12 P CCCCCCCCCC....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5B4A - LP5 C34 H66 N O12 P CCCCCCCCCC....
2 5B49 - LP5 C34 H66 N O12 P CCCCCCCCCC....
3 5B4B - LP5 C34 H66 N O12 P CCCCCCCCCC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: LP5; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 LP5 1 1
2 LP5 LP4 0.663366 0.911765
3 LP4 LP5 0.663366 0.911765
4 LP4 LP5 MYR DAO 0.51145 0.911765
5 U21 0.495935 0.775
6 U20 0.495935 0.775
7 U22 0.415385 0.777778
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5B4B; Ligand: LP5; Similar sites found: 148
This union binding pocket(no: 1) in the query (biounit: 5b4b.bio2) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5N8V KZZ 0.003277 0.45523 None
2 2VWA PTY 0.007633 0.44797 None
3 4ZOM 4Q3 0.00192 0.44614 None
4 4JMU 1ML 0.00952 0.43602 None
5 4LWU 20U 0.0162 0.40778 None
6 1UVC STE 0.002697 0.40773 None
7 1TV5 N8E 0.0001072 0.55898 0.806452
8 1I0B PEL 0.03146 0.4088 1.6129
9 3KP6 SAL 0.02281 0.41692 1.98676
10 3W54 RNB 0.01312 0.40531 2.01613
11 1FK5 OLA 0.001522 0.43315 2.15054
12 1TLG GAL 0.01228 0.41745 2.4
13 2HHP FLC 0.0001391 0.4836 2.41935
14 3R9V DXC 0.002818 0.46805 2.41935
15 4G8R 96P 0.01754 0.42342 2.41935
16 5VRH OLB 0.02857 0.41286 2.49042
17 2YJD YJD 0.006503 0.42303 2.5
18 3SQP 3J8 0.04476 0.40103 2.51046
19 1H0A I3P 0.0329 0.41311 2.53165
20 3E3U NVC 0.008853 0.42043 2.53807
21 3SHZ 5CO 0.01739 0.41371 2.59366
22 1X0P FAD 0.002357 0.44806 2.7972
23 5LX9 OLB 0.002754 0.44481 2.82258
24 5IXK 6EW 0.002053 0.40054 2.82258
25 4XPL ACO 0.007079 0.41768 3.06748
26 3L1N PLM 0.001249 0.4827 3.09278
27 3TL1 JRO 0.01135 0.43197 3.14465
28 2CHT TSA 0.04078 0.40228 3.14961
29 1TMX HGX 0.002984 0.42406 3.22581
30 4ARE FLC 0.03947 0.40607 3.22581
31 5AZC PGT 0.02055 0.40509 3.22581
32 5K53 STE 0.003367 0.42521 3.43511
33 3FUR Z12 0.0008882 0.44179 3.62903
34 3G9E RO7 0.0004289 0.44137 3.62903
35 5TWO 7MV 0.005759 0.41491 3.62903
36 3RDE OYP 0.007498 0.40375 3.62903
37 2VDY HCY 0.02084 0.41929 3.75335
38 1DKF BMS 0.003627 0.41715 3.82979
39 5V4R MGT 0.002722 0.47679 4.03226
40 5MBC FMN 0.00114 0.45856 4.03226
41 1XMY ROL 0.00819 0.4347 4.03226
42 1XM4 PIL 0.01043 0.42085 4.03226
43 5FQK 6NT 0.02648 0.4147 4.03226
44 2QES ADE 0.03144 0.40981 4.03226
45 1XMU ROF 0.01662 0.40724 4.03226
46 4NB5 2JT 0.002318 0.43608 4.09357
47 4HBM 0Y7 0.01708 0.40667 4.16667
48 3IX9 MTX 0.02107 0.40575 4.21053
49 4UCC ZKW 0.01021 0.44974 4.29185
50 3N7S 3N7 0.01848 0.43178 4.34783
51 1M2Z BOG 0.0003109 0.51618 4.43548
52 4OAR 2S0 0.001132 0.4461 4.43548
53 3SP6 IL2 0.001819 0.44082 4.43548
54 3KDU NKS 0.00229 0.42703 4.43548
55 1K7L 544 0.001972 0.41881 4.43548
56 1NHZ 486 0.004977 0.41772 4.43548
57 4X8D AVI 0.02097 0.41574 4.43548
58 3FEI CTM 0.003432 0.41505 4.43548
59 2FDW D3G 0.02133 0.41316 4.43548
60 2NPA MMB 0.004298 0.41097 4.43548
61 1SR7 MOF 0.002514 0.40898 4.43548
62 5B25 4QJ 0.006375 0.40383 4.43548
63 5DCH 1YO 0.001614 0.48056 4.6875
64 2HJ3 FAD 0.003978 0.41866 4.8
65 2Z7I 742 0.009441 0.4141 4.83871
66 5AHS COA 0.01418 0.41057 4.83871
67 1BII ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 0.004144 0.40049 4.83871
68 4URN NOV 0.03456 0.40615 4.88889
69 3G5K BB2 0.01883 0.40462 4.91803
70 1GUX ASP LEU TYR CYS TYR GLU GLN LEU ASN 0.01614 0.40441 5.04587
71 5L2J 70E 0.0002342 0.48154 5.10204
72 5L2J 6UL 0.0002149 0.48154 5.10204
73 2BYC FMN 0.004327 0.43539 5.10949
74 4OAS 2SW 0.007978 0.42261 5.20833
75 5CX6 CDP 0.007169 0.44501 5.24194
76 5HCN DAO 0.00684 0.44363 5.24194
77 2Q2Y MKR 0.004542 0.4319 5.24194
78 2Q2Y ADP 0.004542 0.4319 5.24194
79 1J78 VDY 0.01683 0.41851 5.24194
80 4WOE 3S5 0.01903 0.41468 5.24194
81 2WH8 II2 0.02229 0.41216 5.24194
82 3RY9 1CA 0.01083 0.40916 5.24194
83 2JHP GUN 0.01222 0.40903 5.24194
84 3G5D 1N1 0.008719 0.40736 5.24194
85 1Q8A HCS 0.03572 0.40676 5.24194
86 3HR1 PF9 0.007728 0.40616 5.24194
87 1RDT 570 0.002238 0.41963 5.3719
88 1RDT L79 0.007181 0.41068 5.3719
89 3HP9 CF1 0.004588 0.4669 5.64516
90 3BOF HCS 0.04565 0.40111 5.64516
91 3AQT RCO 0.01477 0.42702 5.71429
92 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 0.01213 0.42161 5.71429
93 4YV5 SVR 0.01945 0.41855 5.7377
94 4MGA 27L 0.00232 0.47747 6.04839
95 2BJ4 OHT 0.0008975 0.45054 6.04839
96 4TV1 36M 0.005096 0.4504 6.04839
97 5HYR EST 0.005456 0.43055 6.04839
98 4TUZ 36J 0.01501 0.41305 6.04839
99 4MG7 27H 0.01165 0.4077 6.04839
100 4MG8 27J 0.01793 0.40564 6.04839
101 1QY8 RDI 0.01642 0.40406 6.04839
102 3UUD EST 0.02023 0.40311 6.04839
103 5DXE EST 0.02262 0.40075 6.04839
104 4IBF 1D5 0.006425 0.42713 6.20155
105 3T50 FMN 0.006895 0.41475 6.25
106 4DOO DAO 0.005099 0.42424 6.34146
107 1ID0 ANP 0.01198 0.41788 6.57895
108 2PRG BRL 0.007594 0.41627 6.81818
109 4V3I ASP LEU THR ARG PRO 0.007943 0.44553 6.85484
110 1VPD TLA 0.009478 0.43975 6.85484
111 2QJY UQ2 0.01855 0.42357 6.95187
112 3L9R L9R 0.0005512 0.41308 7.14286
113 4B6C B5U 0.01287 0.40907 7.14286
114 2ALG DAO 0.002818 0.42514 7.6087
115 2ALG HP6 0.002818 0.42514 7.6087
116 2WPX ACO 0.00702 0.4144 7.66129
117 4J25 OGA 0.02415 0.41035 7.66129
118 4MRP GSH 0.03145 0.4096 7.66129
119 2WPW ACO 0.01906 0.401 7.66129
120 2Z9I GLY ALA THR VAL 0.04939 0.40654 7.71605
121 2HFN FMN 0.01134 0.40825 7.84314
122 5U98 1KX 0.002564 0.43249 8.06452
123 1WLJ U5P 0.01777 0.4199 8.06452
124 5KK4 44E 0.04536 0.40509 8.33333
125 5MWE TCE 0.003867 0.45675 8.57143
126 5K52 OCD 0.00404 0.41837 8.67924
127 3SHR CMP 0.02756 0.40355 8.87097
128 3KO0 TFP 0.04174 0.40929 8.91089
129 3TDC 0EU 0.00002928 0.62984 9.27419
130 4DXD 9PC 0.01198 0.40083 9.67742
131 1N13 AG2 0.03777 0.40575 9.73451
132 2QQC AG2 0.0328 0.40921 9.82143
133 2QQD AG2 0.03474 0.40604 9.82143
134 1XVB 3BR 0.004292 0.44436 10.0806
135 5CHR 4NC 0.003578 0.46043 10.219
136 3B6C SDN 0.002222 0.46948 10.6838
137 2WDA L42 0.02 0.42148 11.2903
138 4YSX E23 0.04461 0.40018 11.6935
139 4J6C STR 0.02195 0.41251 12.0968
140 2CB8 MYA 0.01247 0.43225 12.6437
141 5U9J GER 0.03485 0.40596 13.0178
142 5LWY OLB 0.001115 0.46366 14.2857
143 5OCA 9QZ 0.00003941 0.58885 14.7059
144 2Q4G CIT 0.02531 0.41341 15.5039
145 3G08 FEE 0.002898 0.42714 15.7258
146 4I67 G G G RPC 0.002177 0.4592 18.3908
147 3ALT MLB 0.01026 0.43462 22.9299
148 2XN5 FUN 0.002373 0.45731 31.4286
Pocket No.: 2; Query (leader) PDB : 5B4B; Ligand: LP5; Similar sites found: 51
This union binding pocket(no: 2) in the query (biounit: 5b4b.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WG0 CHD 0.03952 0.40767 None
2 1GEG GLC 0.02558 0.41404 1.6129
3 4WGF HX2 0.03128 0.40985 1.95122
4 5EE7 5MV 0.02334 0.41697 2.01613
5 2HFK E4H 0.02434 0.41553 2.01613
6 3BEJ MUF 0.008686 0.40233 2.10084
7 3OKI OKI 0.008526 0.40868 2.14592
8 5ICK FEZ 0.01448 0.40145 2.18341
9 2Q4X HMH 0.03987 0.40431 2.26244
10 4B1X LAB 0.02757 0.40854 2.41935
11 4B1Y LAB 0.03202 0.40514 2.41935
12 1U3R 338 0.002574 0.43929 2.48963
13 4M8E 29V 0.005937 0.40939 3.4632
14 4POJ 2VP 0.008265 0.40042 3.4632
15 4XCP PLM 0.03467 0.40703 3.52941
16 3KMR EQN 0.01023 0.40829 3.62903
17 4DHL 0K7 0.003396 0.46625 4.03226
18 2YFB SIN 0.008985 0.40601 4.03226
19 2YOR MZ0 0.0007982 0.40348 4.03226
20 1II7 DA 0.01357 0.43176 4.43548
21 1CZA ADP 0.02767 0.41763 4.43548
22 5HCV 60R 0.007604 0.41089 5.24194
23 1J78 OLA 0.006149 0.41011 5.24194
24 5MES 7LT 0.004454 0.44039 5.30973
25 3FAL REA 0.002872 0.44533 5.3719
26 1FBY REA 0.006484 0.40484 5.43933
27 1FM9 9CR 0.007767 0.41048 5.46218
28 2W3L DRO 0.03936 0.40424 5.55556
29 5MOB A8S 0.02034 0.41148 5.60345
30 2Q1H AS4 0.006773 0.41642 5.64516
31 1T0S BML 0.03746 0.40301 5.81395
32 3UUA 0CZ 0.01162 0.42383 6.04839
33 4MGB XDH 0.00601 0.42228 6.04839
34 3P9T TCL 0.03255 0.40105 6.39269
35 4PEG 5GP 0.008679 0.44932 6.45161
36 3RLF MAL 0.02124 0.41448 7.66129
37 2X1L MET 0.02796 0.41164 8.06452
38 2CDO GAL AAL GAL AAL GAL AAL 0.02291 0.41168 8.125
39 3ZVS MLI 0.03093 0.40496 8.125
40 1YRX FMN 0.005961 0.42614 8.26446
41 1YC4 43P 0.006189 0.43334 8.33333
42 3GQT UFO 0.02697 0.40163 9.27419
43 4ZGM 32M 0.005261 0.45771 10.6557
44 5V49 MET 0.02545 0.41037 10.8871
45 3WFD AXO 0.0112 0.41923 10.9589
46 2ZJ5 ADP 0.014 0.43035 11.2903
47 1S14 NOV 0.03454 0.40735 11.3402
48 2ZO9 MLI 0.009892 0.43567 12.9032
49 4V1T ADP 0.01776 0.40047 14.1129
50 3CV2 COA 0.048 0.40913 14.9194
51 2Y69 CHD 0.03607 0.40865 18.75
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