FAIRMol

Z1162463429

Pose ID 3354 Compound 1545 Pose 644

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 Z1162463429
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
16.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.53, Jaccard 0.47, H-bond role recall 0.17
Burial
95%
Hydrophobic fit
70%
Reason: no major geometry red flags detected
1 protein-contact clashes 40% of hydrophobic surface appears solvent-exposed (4/10 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 (-1.665 kcal/mol/HA) ✓ Good fit quality (FQ -13.02) ✓ Good H-bonds (5 bonds) ✓ Deep burial (95% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ Moderate strain (16.7 kcal/mol) ✗ Geometry warnings
Score
-28.301
kcal/mol
LE
-1.665
kcal/mol/HA
Fit Quality
-13.02
FQ (Leeson)
HAC
17
heavy atoms
MW
242
Da
LogP
-1.51
cLogP
Final rank
1.5927
rank score
Inter norm
-1.747
normalised
Contacts
11
H-bonds 5
Strain ΔE
16.7 kcal/mol
SASA buried
95%
Lipo contact
70% BSA apolar/total
SASA unbound
438 Ų
Apolar buried
290 Ų

Interaction summary

HBD 1 HBA 4 HY 4 PI 1 CLASH 1

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

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
Jaccard0.47RMSD-
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
645 -0.24535152299569776 -1.45581 -24.4873 3 9 9 0.53 0.17 - no Open
654 0.7169325932667672 -1.79088 -28.7768 10 11 0 0.00 0.00 - no Open
644 1.5926986183612593 -1.74651 -28.3012 5 11 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 -28.301kcal/mol
Ligand efficiency (LE) -1.6648kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -13.018
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 17HA

Physicochemical properties
Molecular weight 242.2Da
Lipinski: ≤ 500 Da
LogP (cLogP) -1.51
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 16.70kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -70.82kcal/mol
Minimised FF energy -87.51kcal/mol

SASA & burial

✓ computed
SASA (unbound) 437.9Ų
Total solvent-accessible surface area of free ligand
BSA total 417.3Ų
Buried surface area upon binding
BSA apolar 290.3Ų
Hydrophobic contacts buried
BSA polar 127.0Ų
Polar contacts buried
Fraction buried 95.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 69.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1462.5Ų
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 1018.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)