FAIRMol

Z19657359

Pose ID 2626 Compound 1843 Pose 593

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 Z19657359
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
24.6 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.58, Jaccard 0.58, H-bond role recall 0.20
Burial
84%
Hydrophobic fit
72%
Reason: no major geometry red flags detected
1 protein-contact clashes 35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.968 kcal/mol/HA) ✓ Good fit quality (FQ -8.67) ✓ Deep burial (84% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ High strain energy (24.6 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-23.230
kcal/mol
LE
-0.968
kcal/mol/HA
Fit Quality
-8.67
FQ (Leeson)
HAC
24
heavy atoms
MW
337
Da
LogP
2.34
cLogP
Final rank
1.7022
rank score
Inter norm
-1.189
normalised
Contacts
11
H-bonds 2
Strain ΔE
24.6 kcal/mol
SASA buried
84%
Lipo contact
72% BSA apolar/total
SASA unbound
550 Ų
Apolar buried
331 Ų

Interaction summary

HBA 2 HY 4 PI 4 CLASH 2

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

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 overlap11Native recall0.58
Jaccard0.58RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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
593 1.7022323763965452 -1.18904 -23.2299 2 11 11 0.58 0.20 - no Current
590 3.451046405198834 -1.35741 -31.596 11 12 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 -23.230kcal/mol
Ligand efficiency (LE) -0.9679kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.674
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 337.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.34
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 24.60kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 84.79kcal/mol
Minimised FF energy 60.19kcal/mol

SASA & burial

✓ computed
SASA (unbound) 550.5Ų
Total solvent-accessible surface area of free ligand
BSA total 460.1Ų
Buried surface area upon binding
BSA apolar 331.0Ų
Hydrophobic contacts buried
BSA polar 129.1Ų
Polar contacts buried
Fraction buried 83.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1576.3Ų
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 1023.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)