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4RZ8
Biol. Unit 2
Info
Asym.Unit (496 KB)
Biol.Unit 1 (126 KB)
Biol.Unit 2 (124 KB)
Biol.Unit 3 (126 KB)
Biol.Unit 4 (126 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HIV-1 GP120 CORE IN COMPLEX WITH NBD-11021, A SMALL MOLECULE CD4-ANTAGONIST
Authors
:
Y. D. Kwon, A. K. Debnath, P. D. Kwong
Date
:
18 Dec 14 (Deposition) - 09 Sep 15 (Release) - 23 Sep 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Hiv-1 Gp120, Nbd-11021, Small Molecule Cd4-Antagonist, Phe 43 Cavity, Viral Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. Curreli, Y. D. Kwon, H. Zhang, D. Scacalossi, D. S. Belov, A. A. Tikhonov, I. A. Andreev, A. Altieri, A. V. Kurkin, P. D. Kwong, A. K. Debnath
Structure-Based Design Of A Small Molecule Cd4-Antagonist With Broad Spectrum Anti-Hiv-1 Activity.
J. Med. Chem. V. 58 6909 2015
[
close entry info
]
Hetero Components
(3, 11)
Info
All Hetero Components
1a: 5-(4-CHLOROPHENYL)-N-{(S)-[5-(HYDR... (3ZMa)
1b: 5-(4-CHLOROPHENYL)-N-{(S)-[5-(HYDR... (3ZMb)
1c: 5-(4-CHLOROPHENYL)-N-{(S)-[5-(HYDR... (3ZMc)
1d: 5-(4-CHLOROPHENYL)-N-{(S)-[5-(HYDR... (3ZMd)
2a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
2b: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEb)
2c: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEc)
2d: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEd)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3aa: N-ACETYL-D-GLUCOSAMINE (NAGaa)
3ab: N-ACETYL-D-GLUCOSAMINE (NAGab)
3ac: N-ACETYL-D-GLUCOSAMINE (NAGac)
3ad: N-ACETYL-D-GLUCOSAMINE (NAGad)
3ae: N-ACETYL-D-GLUCOSAMINE (NAGae)
3af: N-ACETYL-D-GLUCOSAMINE (NAGaf)
3ag: N-ACETYL-D-GLUCOSAMINE (NAGag)
3ah: N-ACETYL-D-GLUCOSAMINE (NAGah)
3ai: N-ACETYL-D-GLUCOSAMINE (NAGai)
3aj: N-ACETYL-D-GLUCOSAMINE (NAGaj)
3ak: N-ACETYL-D-GLUCOSAMINE (NAGak)
3al: N-ACETYL-D-GLUCOSAMINE (NAGal)
3am: N-ACETYL-D-GLUCOSAMINE (NAGam)
3an: N-ACETYL-D-GLUCOSAMINE (NAGan)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3g: N-ACETYL-D-GLUCOSAMINE (NAGg)
3h: N-ACETYL-D-GLUCOSAMINE (NAGh)
3i: N-ACETYL-D-GLUCOSAMINE (NAGi)
3j: N-ACETYL-D-GLUCOSAMINE (NAGj)
3k: N-ACETYL-D-GLUCOSAMINE (NAGk)
3l: N-ACETYL-D-GLUCOSAMINE (NAGl)
3m: N-ACETYL-D-GLUCOSAMINE (NAGm)
3n: N-ACETYL-D-GLUCOSAMINE (NAGn)
3o: N-ACETYL-D-GLUCOSAMINE (NAGo)
3p: N-ACETYL-D-GLUCOSAMINE (NAGp)
3q: N-ACETYL-D-GLUCOSAMINE (NAGq)
3r: N-ACETYL-D-GLUCOSAMINE (NAGr)
3s: N-ACETYL-D-GLUCOSAMINE (NAGs)
3t: N-ACETYL-D-GLUCOSAMINE (NAGt)
3u: N-ACETYL-D-GLUCOSAMINE (NAGu)
3v: N-ACETYL-D-GLUCOSAMINE (NAGv)
3w: N-ACETYL-D-GLUCOSAMINE (NAGw)
3x: N-ACETYL-D-GLUCOSAMINE (NAGx)
3y: N-ACETYL-D-GLUCOSAMINE (NAGy)
3z: N-ACETYL-D-GLUCOSAMINE (NAGz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3ZM
1
Ligand/Ion
5-(4-CHLOROPHENYL)-N-{(S)-[5-(HYDROXYMETHYL)-4-METHYL-1,3-THIAZOL-2-YL][(2R)-PIPERIDIN-2-YL]METHYL}-1H-PYRROLE-2-CARBOXAMIDE
2
EPE
1
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3
NAG
9
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(15, 15)
Info
All Sites
01: AC8 (SOFTWARE)
02: BC2 (SOFTWARE)
03: BC3 (SOFTWARE)
04: BC4 (SOFTWARE)
05: BC5 (SOFTWARE)
06: BC6 (SOFTWARE)
07: BC7 (SOFTWARE)
08: BC8 (SOFTWARE)
09: BC9 (SOFTWARE)
10: CC1 (SOFTWARE)
11: CC2 (SOFTWARE)
12: CC3 (SOFTWARE)
13: CC4 (SOFTWARE)
14: CC8 (SOFTWARE)
15: DC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC8
SOFTWARE
MET A:373 , ASN A:386 , THR A:388 , GLN B:203
BINDING SITE FOR RESIDUE NAG A 508
02
BC2
SOFTWARE
LEU A:52 , CYS A:54 , ALA A:73 , GLN A:103 , ASP A:107 , TYR A:217 , ARG B:327 , LYS B:421 , GLN B:422 , ILE B:423
BINDING SITE FOR RESIDUE EPE A 511
03
BC3
SOFTWARE
ASN B:234 , THR B:236 , HIS B:352
BINDING SITE FOR RESIDUE NAG B 501
04
BC4
SOFTWARE
ASN B:229 , ASN B:241
BINDING SITE FOR RESIDUE NAG B 502
05
BC5
SOFTWARE
LEU B:261 , ASN B:262 , ARG B:379 , CYS B:445 , VAL B:446 , SER B:447 , NAG B:509 , HOH B:603 , HOH B:606 , HOH B:610 , HOH B:616 , ASN C:354 , ASN C:355 , SER C:464
BINDING SITE FOR RESIDUE NAG B 503
06
BC6
SOFTWARE
ASN B:276 , ASN B:279
BINDING SITE FOR RESIDUE NAG B 504
07
BC7
SOFTWARE
GLU B:268 , ILE B:270 , ASN B:289
BINDING SITE FOR RESIDUE NAG B 505
08
BC8
SOFTWARE
ASN B:295 , TYR B:330 , VAL B:446 , HOH B:660 , HOH C:703 , HOH C:747
BINDING SITE FOR RESIDUE NAG B 506
09
BC9
SOFTWARE
ASN B:334 , LYS B:337 , THR B:413 , HOH B:712
BINDING SITE FOR RESIDUE NAG B 507
10
CC1
SOFTWARE
ASN B:386 , THR B:388
BINDING SITE FOR RESIDUE NAG B 508
11
CC2
SOFTWARE
ASN B:262 , ASN B:448 , NAG B:503 , HOH B:613 , HOH B:685 , HOH B:719 , LYS C:350 , ASN C:355
BINDING SITE FOR RESIDUE NAG B 509
12
CC3
SOFTWARE
VAL B:255 , ASP B:368 , GLU B:370 , SER B:375 , PHE B:376 , ASN B:377 , ASN B:425 , MET B:426 , TRP B:427 , GLN B:428 , GLY B:429
BINDING SITE FOR RESIDUE 3ZM B 510
13
CC4
SOFTWARE
ARG A:327 , LYS A:421 , GLN A:422 , ILE A:423 , LEU B:52 , CYS B:54 , HIS B:72 , ALA B:73 , GLN B:103 , ASP B:107
BINDING SITE FOR RESIDUE EPE B 511
14
CC8
SOFTWARE
HIS B:61 , ASN C:276 , THR C:278 , ASN C:279
BINDING SITE FOR RESIDUE NAG C 504
15
DC3
SOFTWARE
LYS B:252 , ASN C:354 , ASN C:355 , HOH C:660 , HOH C:701
BINDING SITE FOR RESIDUE NAG C 508
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
Info
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;
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
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Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
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Sorry, no Info available
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Atom Selection
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All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain B
Asymmetric Unit 1
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select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
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Show PDB file:
Asym.Unit (496 KB)
Header - Asym.Unit
Biol.Unit 1 (126 KB)
Header - Biol.Unit 1
Biol.Unit 2 (124 KB)
Header - Biol.Unit 2
Biol.Unit 3 (126 KB)
Header - Biol.Unit 3
Biol.Unit 4 (126 KB)
Header - Biol.Unit 4
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