FAIRMol

Z19574276

Pose ID 2438 Compound 1640 Pose 405

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 Z19574276
PDB7PXX↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry high Native strong SASA done
Strain ΔE
22.2 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.74, Jaccard 0.74, H-bond role recall 0.00
Burial
76%
Hydrophobic fit
86%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.849 kcal/mol/HA) ✓ Good fit quality (FQ -8.10) ✓ Deep burial (76% SASA buried) ✓ Lipophilic contacts well-matched (86%) ✗ High strain energy (22.2 kcal/mol) ✗ No H-bonds detected ✗ Geometry warnings ✗ Internal clashes (9)
Score
-24.621
kcal/mol
LE
-0.849
kcal/mol/HA
Fit Quality
-8.10
FQ (Leeson)
HAC
29
heavy atoms
MW
443
Da
LogP
5.77
cLogP
Final rank
0.2854
rank score
Inter norm
-0.908
normalised
Contacts
14
H-bonds 1
Strain ΔE
22.2 kcal/mol
SASA buried
76%
Lipo contact
86% BSA apolar/total
SASA unbound
661 Ų
Apolar buried
438 Ų

Interaction summary

HB 0 HY 8 PI 3 CLASH 2

HBD/HBA · H-bonds (geometric)
No hbd/hba · h-bonds (geometric) detected for this pose.

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: permissive.
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 overlap14Native recall0.74
Jaccard0.74RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
405 0.2853552136087226 -0.907637 -24.6214 1 14 14 0.74 0.00 - no Current
417 1.8230804083906484 -0.703539 -21.9002 7 11 0 0.00 0.00 - no Open
417 2.6132480506910896 -0.942434 -23.9627 5 16 0 0.00 0.00 - no Open
368 2.9426670215919564 -1.14768 -32.7619 7 23 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 -24.621kcal/mol
Ligand efficiency (LE) -0.8490kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.104
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 443.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.77
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 22.22kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 71.46kcal/mol
Minimised FF energy 49.24kcal/mol

SASA & burial

✓ computed
SASA (unbound) 661.3Ų
Total solvent-accessible surface area of free ligand
BSA total 506.1Ų
Buried surface area upon binding
BSA apolar 438.0Ų
Hydrophobic contacts buried
BSA polar 68.2Ų
Polar contacts buried
Fraction buried 76.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 86.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1732.8Ų
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 1037.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)