FAIRMol

NMT-TY0624

Pose ID 5032 Compound 616 Pose 291

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
T08
T. brucei PTR1 T. brucei
Ligand NMT-TY0624
PDB6RX6↗

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 medium Native strong SASA done
Strain ΔE
38.3 kcal/mol
Protein clashes
2
Internal clashes
5
Native overlap
contact recall 0.58, Jaccard 0.52, H-bond role recall 0.40
Burial
89%
Hydrophobic fit
69%
Reason: no major geometry red flags detected
2 protein-contact clashes 5 intramolecular clashes 38% of hydrophobic surface appears solvent-exposed (6/16 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 (-1.192 kcal/mol/HA) ✓ Good fit quality (FQ -10.98) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (89% SASA buried) ✓ Lipophilic contacts well-matched (69%) ✗ Very high strain energy (38.3 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (2) ✗ Many internal clashes (12)
Score
-30.995
kcal/mol
LE
-1.192
kcal/mol/HA
Fit Quality
-10.98
FQ (Leeson)
HAC
26
heavy atoms
MW
396
Da
LogP
2.16
cLogP
Strain ΔE
38.3 kcal/mol
SASA buried
89%
Lipo contact
69% BSA apolar/total
SASA unbound
617 Ų
Apolar buried
379 Ų

Interaction summary

HB 10 HY 14 PI 2 CLASH 5 ⚠ Exposure 37%

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
⚠️Partial hydrophobic solvent exposure
38% of hydrophobic surface appears solvent-exposed (6/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 16 Buried (contacted) 10 Exposed 6 LogP 2.16 H-bonds 10
Exposed fragments: phenyl (6/6 atoms exposed)
Final rank0.632Score-30.995
Inter norm-1.220Intra norm0.028
Top1000noExcludedno
Contacts13H-bonds10
Artifact reasongeometry warning; 12 clashes; 2 protein contact clashes; 2 severe cofactor-context clashes; high strain Δ 38.3
Residues
ARG14 ASP161 CYS168 LEU208 LEU209 LYS13 NAP301 PHE97 PRO210 SER95 TRP221 TYR174 VAL211

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameTbPTR1_cW_6RX6_ReadyContacts19
PoseOpen native poseHB0
IFP residues
ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LYS178 MET213 NAP301 PHE171 PHE97 PRO210 PRO99 SER207 SER95 TRP221 TYR174 TYR98 VAL206
Current overlap11Native recall0.58
Jaccard0.52RMSD-
HB strict3Strict recall0.50
HB same residue+role2HB role recall0.40
HB same residue3HB residue recall0.60

Protein summary

258 residues
Protein targetT08Atoms3881
Residues258Chains2
Residue summaryLEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103

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:NAP301

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
323 0.604003958058523 -0.942657 -21.1902 4 15 0 0.00 0.00 - no Open
291 0.6323186320960439 -1.22038 -30.9952 10 13 11 0.58 0.40 - no Current
329 1.875810958250805 -0.873591 -23.2439 4 10 0 0.00 0.00 - no Open
290 2.002828557753335 -1.14993 -29.8501 9 14 0 0.00 0.00 - no Open
310 2.224044674964138 -0.998085 -25.5439 8 18 0 0.00 0.00 - no Open
274 2.2594370727836455 -1.19735 -30.4625 8 17 0 0.00 0.00 - no Open
363 2.3368706908166565 -1.24065 -32.9492 6 14 0 0.00 0.00 - no Open
296 2.3850699368176747 -1.30385 -33.7876 14 22 0 0.00 0.00 - no Open
256 2.4947555472898184 -0.974719 -18.8557 12 13 0 0.00 0.00 - no Open
354 2.712760058770864 -1.25519 -32.5296 10 15 0 0.00 0.00 - no Open
425 3.1536405973770054 -1.02037 -26.076 10 16 0 0.00 0.00 - no Open
270 3.5240590701875685 -1.13687 -30.0974 8 15 0 0.00 0.00 - no Open
349 3.8084335922387926 -0.992658 -26.3696 8 20 0 0.00 0.00 - no Open
380 3.892965236960112 -1.26373 -32.5926 8 16 0 0.00 0.00 - no Open
394 4.604769733373062 -0.872118 -21.6077 9 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 -30.995kcal/mol
Ligand efficiency (LE) -1.1921kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.983
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 395.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.16
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 38.28kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -10.69kcal/mol
Minimised FF energy -48.97kcal/mol

SASA & burial

✓ computed
SASA (unbound) 617.0Ų
Total solvent-accessible surface area of free ligand
BSA total 546.4Ų
Buried surface area upon binding
BSA apolar 378.8Ų
Hydrophobic contacts buried
BSA polar 167.7Ų
Polar contacts buried
Fraction buried 88.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 69.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1579.5Ų
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 2051.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 917.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)