FAIRMol

Z19455379

Pose ID 3077 Compound 2214 Pose 367

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 Z19455379
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
18.0 kcal/mol
Protein clashes
2
Internal clashes
4
Native overlap
contact recall 0.65, Jaccard 0.58, H-bond role recall 0.33
Burial
86%
Hydrophobic fit
56%
Reason: no major geometry red flags detected
2 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.165 kcal/mol/HA) ✓ Good fit quality (FQ -10.44) ✓ Good H-bonds (5 bonds) ✓ Deep burial (86% SASA buried) ✗ Moderate strain (18.0 kcal/mol) ✗ Geometry warnings
Score
-27.947
kcal/mol
LE
-1.165
kcal/mol/HA
Fit Quality
-10.44
FQ (Leeson)
HAC
24
heavy atoms
MW
344
Da
LogP
1.88
cLogP
Final rank
2.8650
rank score
Inter norm
-1.272
normalised
Contacts
13
H-bonds 9
Strain ΔE
18.0 kcal/mol
SASA buried
86%
Lipo contact
56% BSA apolar/total
SASA unbound
578 Ų
Apolar buried
276 Ų

Interaction summary

HBD 1 HBA 4 PC 2 HY 5 PI 2 CLASH 4

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.

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: strict.
NameligandContacts17
PoseOpen native poseHB0
IFP residues
ARG17 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap11Native recall0.65
Jaccard0.58RMSD-
HB strict2Strict recall0.29
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
390 2.0969916405130395 -0.997623 -20.9576 7 17 0 0.00 0.00 - no Open
367 2.864983455248954 -1.27194 -27.9472 9 13 11 0.65 0.33 - no Current
416 2.951946838060597 -1.16437 -26.3565 6 15 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 -27.947kcal/mol
Ligand efficiency (LE) -1.1645kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.436
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 344.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.88
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 17.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 64.22kcal/mol
Minimised FF energy 46.26kcal/mol

SASA & burial

✓ computed
SASA (unbound) 578.2Ų
Total solvent-accessible surface area of free ligand
BSA total 495.2Ų
Buried surface area upon binding
BSA apolar 276.2Ų
Hydrophobic contacts buried
BSA polar 219.0Ų
Polar contacts buried
Fraction buried 85.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 55.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1484.7Ų
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 1025.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)