FAIRMol

Z57676781

Pose ID 2679 Compound 1853 Pose 646

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 Z57676781
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 but geometrically suspicious
Binding strong Geometry low Native mixed SASA done
Strain ΔE
10.2 kcal/mol
Protein clashes
5
Internal clashes
6
Native overlap
contact recall 0.53, Jaccard 0.53, H-bond role recall 0.20
Burial
81%
Hydrophobic fit
76%
Reason: 6 internal clashes
5 protein-contact clashes 6 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.065 kcal/mol/HA) ✓ Good fit quality (FQ -9.55) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ Moderate strain (10.2 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-25.571
kcal/mol
LE
-1.065
kcal/mol/HA
Fit Quality
-9.55
FQ (Leeson)
HAC
24
heavy atoms
MW
379
Da
LogP
4.77
cLogP
Final rank
1.7793
rank score
Inter norm
-1.067
normalised
Contacts
10
H-bonds 3
Strain ΔE
10.2 kcal/mol
SASA buried
81%
Lipo contact
76% BSA apolar/total
SASA unbound
570 Ų
Apolar buried
349 Ų

Interaction summary

HBA 1 PC 2 HY 5 PI 4 CLASH 6

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 1.

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.
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 overlap10Native recall0.53
Jaccard0.53RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
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
646 1.7793144131990835 -1.06676 -25.5714 3 10 10 0.53 0.20 - no Current
640 2.8232917357122225 -0.945054 -19.5474 2 12 0 0.00 0.00 - no Open
653 4.513969588477552 -0.960122 -20.5267 7 19 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 -25.571kcal/mol
Ligand efficiency (LE) -1.0655kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.549
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 379.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.77
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 10.19kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 84.11kcal/mol
Minimised FF energy 73.92kcal/mol

SASA & burial

✓ computed
SASA (unbound) 570.0Ų
Total solvent-accessible surface area of free ligand
BSA total 460.9Ų
Buried surface area upon binding
BSA apolar 349.1Ų
Hydrophobic contacts buried
BSA polar 111.8Ų
Polar contacts buried
Fraction buried 80.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 75.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1573.8Ų
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 1061.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)