FAIRMol

Z46095617

Pose ID 3099 Compound 2050 Pose 389

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
T05
L. major PTR1 L. major
Ligand Z46095617
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 strong SASA done
Strain ΔE
14.5 kcal/mol
Protein clashes
1
Internal clashes
3
Native overlap
contact recall 0.59, Jaccard 0.53, H-bond role recall 0.33
Burial
83%
Hydrophobic fit
70%
Reason: no major geometry red flags detected
1 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.131 kcal/mol/HA) ✓ Good fit quality (FQ -9.65) ✓ Good H-bonds (5 bonds) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ Moderate strain (14.5 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-23.760
kcal/mol
LE
-1.131
kcal/mol/HA
Fit Quality
-9.65
FQ (Leeson)
HAC
21
heavy atoms
MW
286
Da
LogP
2.45
cLogP
Final rank
1.4743
rank score
Inter norm
-1.334
normalised
Contacts
12
H-bonds 12
Strain ΔE
14.5 kcal/mol
SASA buried
83%
Lipo contact
70% BSA apolar/total
SASA unbound
547 Ų
Apolar buried
319 Ų

Interaction summary

HBD 1 HBA 4 PC 1 HY 4 PI 1 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.

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.
NameligandContacts17
PoseOpen native poseHB0
IFP residues
ARG17 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap10Native recall0.59
Jaccard0.53RMSD-
HB strict3Strict recall0.43
HB same residue+role2HB role recall0.33
HB same residue3HB residue recall0.60

Protein summary

274 residues
Protein targetT05Atoms4108
Residues274Chains2
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
389 1.4743464540953943 -1.3341 -23.7604 12 12 10 0.59 0.33 - no Current
409 1.7124923188284504 -1.30316 -24.2543 8 19 0 0.00 0.00 - no Open
404 2.308109708434458 -1.32065 -24.0341 9 17 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 -23.760kcal/mol
Ligand efficiency (LE) -1.1314kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.651
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 21HA

Physicochemical properties
Molecular weight 286.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.45
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 14.52kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 20.88kcal/mol
Minimised FF energy 6.36kcal/mol

SASA & burial

✓ computed
SASA (unbound) 547.5Ų
Total solvent-accessible surface area of free ligand
BSA total 453.9Ų
Buried surface area upon binding
BSA apolar 319.2Ų
Hydrophobic contacts buried
BSA polar 134.7Ų
Polar contacts buried
Fraction buried 82.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1571.6Ų
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 1019.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)