FAIRMol

Z19315281

Pose ID 2705 Compound 1764 Pose 672

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 Z19315281
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 high Native mixed SASA done
Strain ΔE
11.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.47, Jaccard 0.47, H-bond role recall 0.40
Burial
78%
Hydrophobic fit
67%
Reason: no major geometry red flags detected
1 protein-contact clashes 40% of hydrophobic surface appears solvent-exposed (6/15 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.066 kcal/mol/HA) ✓ Good fit quality (FQ -9.26) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (67%) ✗ Moderate strain (11.5 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-23.454
kcal/mol
LE
-1.066
kcal/mol/HA
Fit Quality
-9.26
FQ (Leeson)
HAC
22
heavy atoms
MW
326
Da
LogP
3.29
cLogP
Final rank
1.1270
rank score
Inter norm
-1.110
normalised
Contacts
9
H-bonds 2
Strain ΔE
11.5 kcal/mol
SASA buried
78%
Lipo contact
67% BSA apolar/total
SASA unbound
541 Ų
Apolar buried
282 Ų

Interaction summary

HBA 2 HY 3 PI 2 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

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.
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 overlap9Native recall0.47
Jaccard0.47RMSD-
HB strict2Strict recall0.33
HB same residue+role2HB role recall0.40
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
672 1.127024781361967 -1.10974 -23.4543 2 9 9 0.47 0.40 - no Current
660 3.2146589377181907 -1.27723 -28.3019 10 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 -23.454kcal/mol
Ligand efficiency (LE) -1.0661kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.256
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 22HA

Physicochemical properties
Molecular weight 326.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.29
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 11.47kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 6.06kcal/mol
Minimised FF energy -5.41kcal/mol

SASA & burial

✓ computed
SASA (unbound) 541.1Ų
Total solvent-accessible surface area of free ligand
BSA total 423.4Ų
Buried surface area upon binding
BSA apolar 282.1Ų
Hydrophobic contacts buried
BSA polar 141.3Ų
Polar contacts buried
Fraction buried 78.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 66.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1507.8Ų
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 1033.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)