Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
18.6 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.58, Jaccard 0.46, H-bond role recall 0.40
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.385 kcal/mol/HA)
✓ Good fit quality (FQ -12.02)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (96% SASA buried)
✓ Lipophilic contacts well-matched (66%)
✗ Moderate strain (18.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-30.463
kcal/mol
LE
-1.385
kcal/mol/HA
Fit Quality
-12.02
FQ (Leeson)
HAC
22
heavy atoms
MW
331
Da
LogP
3.44
cLogP
Interaction summary
HB 8
HY 24
PI 3
CLASH 4
Interaction summary
HB 8
HY 24
PI 3
CLASH 4
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
| Final rank | 2.483 | Score | -30.463 |
|---|---|---|---|
| Inter norm | -1.461 | Intra norm | 0.077 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 8 |
| Artifact reason | geometry warning; 6 clashes; 2 protein clashes | ||
| Residues |
ARG14
ASN175
ASP161
CYS168
GLN166
LEU208
LEU209
MET163
MET213
NAP301
PHE171
PHE97
PRO167
PRO210
TYR174
VAL164
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | TbPTR1_cW_6RX6_Ready | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG14
ASP161
CYS168
GLY205
LEU208
LEU209
LYS178
MET213
NAP301
PHE171
PHE97
PRO210
PRO99
SER207
SER95
TRP221
TYR174
TYR98
VAL206
| ||
| Current overlap | 11 | Native recall | 0.58 |
| Jaccard | 0.46 | RMSD | - |
| HB strict | 2 | Strict recall | 0.33 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 4 | HB residue recall | 0.80 |
Protein summary
258 residues
| Protein target | T08 | Atoms | 3881 |
|---|---|---|---|
| Residues | 258 | Chains | 2 |
| Residue summary | LEU: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
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 498 | 0.277110928238548 | -1.1663 | -24.1398 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 543 | 0.2814085707376848 | -1.28181 | -23.8629 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 497 | 0.3261405134134158 | -1.12693 | -25.036 | 1 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 523 | 0.7425493178553388 | -1.13066 | -24.5514 | 11 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 523 | 1.118607833921333 | -1.20811 | -22.5833 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 510 | 1.3649241206005485 | -1.15 | -20.093 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 488 | 1.4922564307741122 | -1.4707 | -26.2212 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 560 | 1.7657177566461795 | -1.1595 | -25.6991 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 505 | 2.3175673752518597 | -0.992997 | -20.4526 | 5 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 482 | 2.392174964889073 | -1.5365 | -31.914 | 7 | 15 | 11 | 0.58 | 0.40 | - | no | Open |
| 502 | 2.4832411156841925 | -1.46125 | -30.4633 | 8 | 16 | 11 | 0.58 | 0.40 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-30.463kcal/mol
Ligand efficiency (LE)
-1.3847kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.022
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
331.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.44
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.59kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
13.10kcal/mol
Minimised FF energy
-5.49kcal/mol
SASA & burial
✓ computed
SASA (unbound)
559.4Ų
Total solvent-accessible surface area of free ligand
BSA total
536.7Ų
Buried surface area upon binding
BSA apolar
354.7Ų
Hydrophobic contacts buried
BSA polar
182.0Ų
Polar contacts buried
Fraction buried
95.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
66.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1496.6Ų
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
928.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)