FAIRMol

Z57676781

Pose ID 2679 Compound 1853 Pose 646

DB fairmolDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T04
L. major PTR1 L. major
Ligand Z57676781
PDB7PXX↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry medium Native mixed SASA done
Strain ΔE
10.2 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.53, Jaccard 0.53, H-bond role recall 0.20
Burial
81%
Hydrophobic fit
76%
Reason: no major geometry red flags detected
2 protein-contact clashes 3 intramolecular clashes
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Daphnia EC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Algae IC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium Ames Clear DILI Risk
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.065 kcal/mol/HA) ✓ Good fit quality (FQ -9.55) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ Moderate strain (10.2 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-25.571
kcal/mol
LE
-1.065
kcal/mol/HA
Fit Quality
-9.55
FQ (Leeson)
HAC
24
heavy atoms
MW
379
Da
LogP
4.77
cLogP
Final rank
1.7793
rank score
Inter norm
-1.067
normalised
Contacts
10
H-bonds 3
Strain ΔE
10.2 kcal/mol
SASA buried
81%
Lipo contact
76% BSA apolar/total
SASA unbound
570 Ų
Apolar buried
349 Ų

Interaction summary

HBA 1 PC 2 HY 5 PI 4 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 1.

PC · Polar contacts (possible, no H geometry)
HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
Name7PXXContacts19
PoseOpen native poseHB0
IFP residues
ARG17 ASP181 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER112 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap10Native recall0.53
Jaccard0.53RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
HB same residue2HB residue recall0.40

Protein summary

308 residues
Protein targetT04Atoms4210
Residues308Chains3
Residue summaryLEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:NDP302

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
646 1.7793144131990835 -1.06676 -25.5714 3 10 10 0.53 0.20 - no Current
640 2.8232917357122225 -0.945054 -19.5474 2 12 0 0.00 0.00 - no Open
653 4.513969588477552 -0.960122 -20.5267 7 19 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -25.571kcal/mol
Ligand efficiency (LE) -1.0655kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.549
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 379.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.77
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 10.19kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 84.11kcal/mol
Minimised FF energy 73.92kcal/mol

SASA & burial

✓ computed
SASA (unbound) 570.0Ų
Total solvent-accessible surface area of free ligand
BSA total 460.9Ų
Buried surface area upon binding
BSA apolar 349.1Ų
Hydrophobic contacts buried
BSA polar 111.8Ų
Polar contacts buried
Fraction buried 80.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 75.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1573.8Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1061.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)