FAIRMol

Z25102896

Pose ID 3140 Compound 1492 Pose 430

DB SELECTIONDocking 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 Z25102896
PDB7PXX↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Strong hit SASA cached
Strong candidate with consistent geometry
Binding strong Geometry high Native mixed SASA done
Strain ΔE
7.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.53, Jaccard 0.43, H-bond role recall 0.17
Burial
97%
Hydrophobic fit
60%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Strong hit Multiple positive indicators. High-priority candidate for follow-up.
✓ Low conformational strain (7.9 kcal/mol) ✓ Excellent LE (-1.876 kcal/mol/HA) ✓ Good fit quality (FQ -14.67) ✓ Good H-bonds (5 bonds) ✓ Deep burial (97% SASA buried) ✓ Lipophilic contacts well-matched (60%)
Score
-31.894
kcal/mol
LE
-1.876
kcal/mol/HA
Fit Quality
-14.67
FQ (Leeson)
HAC
17
heavy atoms
MW
270
Da
LogP
1.87
cLogP
Final rank
2.2189
rank score
Inter norm
-1.721
normalised
Contacts
13
H-bonds 5
Strain ΔE
7.9 kcal/mol
SASA buried
97%
Lipo contact
60% BSA apolar/total
SASA unbound
479 Ų
Apolar buried
281 Ų

Interaction summary

HBA 5 HY 5 PI 4 CLASH 2

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.
NameligandContacts17
PoseOpen native poseHB0
IFP residues
ARG17 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap9Native recall0.53
Jaccard0.43RMSD-
HB strict1Strict recall0.14
HB same residue+role1HB role recall0.17
HB same residue1HB residue recall0.20

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
465 -0.715826080613341 -1.52913 -23.3728 5 11 11 0.65 0.17 - no Open
430 2.218924922060391 -1.7208 -31.8936 5 13 9 0.53 0.17 - no Current

Molecular metrics

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

Scoring & efficiency
Docking score -31.894kcal/mol
Ligand efficiency (LE) -1.8761kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -14.670
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 17HA

Physicochemical properties
Molecular weight 270.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.87
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 7.88kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -20.90kcal/mol
Minimised FF energy -28.79kcal/mol

SASA & burial

✓ computed
SASA (unbound) 478.7Ų
Total solvent-accessible surface area of free ligand
BSA total 464.9Ų
Buried surface area upon binding
BSA apolar 280.8Ų
Hydrophobic contacts buried
BSA polar 184.1Ų
Polar contacts buried
Fraction buried 97.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 60.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1438.5Ų
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 1022.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)